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skill CX Codex GP ChatGPT official · OpenAI

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

Submits compact ProteomeXchange PROXI requests to fetch datasets, spectra, proteins, and USI examples.

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

What proteomexchange-skill does

This skill sends structured queries to the ProteomeXchange PROXI API. It gathers data on datasets, libraries, peptidoforms, spectra, and USI examples. The tool formats responses as compact markdown summaries by default. This keeps conversation context clean.

Under the hood, the skill runs scripts/rest_request.py by feeding a JSON object to standard input. Collection paths work best with max_items=10, while specific identifier lookups do not need item limits. When you need the entire payload, setting save_raw=true writes the raw output to raw_output_path. No extra packages are needed beyond Python and the bundled script.

Install this if you inspect proteomics data in Codex. If you do not query ProteomeXchange, you will not need it.

What it helps with

  • fetch ProteomeXchange dataset summaries by identifier
  • query peptidoforms, spectra, and peptide-spectrum matches
  • retrieve sample USI entries with an item limit
  • save full PROXI API responses to local raw files

Example prompts for the agent

  • Look up dataset PXD000001 using PROXI
  • List ten USI examples from ProteomeXchange
  • Fetch spectra details and save the full raw payload

How to install proteomexchange-skill

1Skills CLI (Vercel)

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

2Manually: put the files in place

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

For all projects use ~/.agents/skills/

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Questions about proteomexchange-skill

How to install proteomexchange-skill in Codex?

Run npx skills add openai/plugins --skill proteomexchange-skill in your terminal to add the skill to your Codex setup.

What does proteomexchange-skill do?

It submits targeted PROXI queries for proteomics data and returns concise summaries instead of large raw dumps.

What is required to execute the requests?

It requires Python to execute scripts/rest_request.py. No extra third-party libraries are required.

See also

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