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skill CX Codex GP ChatGPT official · OpenAI

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

Fetch a compact TPMI 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 tpmi-phewas-skill -a codex
Open on GitHub

What tpmi-phewas-skill does

This skill accepts one variant as rsid, grch37, grch38, or variant, resolves it to a canonical GRCh38 query, and fetches TPMI PheWAS association results. The response includes the normalized queried variant, association counts, a truncation flag, and a variant URL.

Lookups run through scripts/tpmi_phewas.py, which reads JSON from stdin or a single variant string. It starts with max_results=10; raise that value gradually when the first slice is too short. Set save_raw=true for the full association payload and report the path returned in raw_output_path instead of putting a large array in chat.

The skill handles exactly one variant per lookup, so validate the variant before running it. The setup requires scripts/tpmi_phewas.py and access to TPMI.

What it helps with

  • fetch TPMI PheWAS associations for one variant
  • resolve GRCh37 coordinates to a GRCh38 query
  • accept an rsID or chr:pos-ref-alt variant
  • limit the returned slice with max_results
  • save the full JSON payload to a file

Example prompts for the agent

  • Check TPMI PheWAS for `rs9273363` and give me a concise summary.
  • Look up `{"grch37":"6:162447146-T-C","max_results":10}`.
  • Fetch `{"variant":"6:160540105:T:C","max_results":25,"save_raw":true}` and report `raw_output_path`.

How to install tpmi-phewas-skill

1Skills CLI (Vercel)

npx skills add openai/plugins --skill tpmi-phewas-skill -a codex

2Manually: put the files in place

.agents/skills/tpmi-phewas-skill/SKILL.md

For all projects use ~/.agents/skills/

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Questions about tpmi-phewas-skill

How do I install `tpmi-phewas-skill` in Codex?

Run npx skills add openai/plugins --skill tpmi-phewas-skill. The skill will be available at .agents/skills/tpmi-phewas-skill/SKILL.md.

What does `tpmi-phewas-skill` do?

It accepts one variant in several formats, resolves it to a canonical GRCh38 query, and returns a compact TPMI PheWAS summary with association counts and truncation status.

Which variant formats does the skill support?

Pass exactly one of rsid, grch37, grch38, or variant. Optional fields include max_results, save_raw, raw_output_path, and timeout_sec.

See also

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