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skill CX Codex GP ChatGPT official · OpenAI

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

Queries the MetaboLights archive and returns compact metabolomics study metadata. Helpful when you need quick study discovery directly in your coding agent.

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

What metabolights-skill does

The skill handles targeted queries to MetaboLights to discover metabolomics studies and retrieve their study-level metadata. The agent accesses the studies path to browse records or studies/ to inspect a single entry. Results are rendered as brief markdown summaries instead of large dumps.

Under the hood, queries run through scripts/rest_request.py, reading JSON from standard input. Required parameters are base_url and path. The payload also accepts limits like max_items, page depth, and flags like save_raw to persist files locally. Raw JSON is returned only when explicitly requested.

Install it if you regularly inspect biological datasets and want concise notes.

What it helps with

  • browse the MetaboLights repository for study identifiers
  • inspect metadata summaries for specific MTBLS accessions
  • paginate API requests to avoid fetching large payloads
  • save raw JSON responses to local files on demand

Example prompts for the agent

  • Search the first 10 studies in MetaboLights using path studies
  • Get a summary for study studies/MTBLS1
  • Fetch study studies/MTBLS1 and save the raw JSON output

How to install metabolights-skill

1Skills CLI (Vercel)

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

2Manually: put the files in place

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

For all projects use ~/.agents/skills/

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Questions about metabolights-skill

How to install metabolights-skill in Codex?

Run npx skills add openai/plugins --skill metabolights-skill in your terminal. Codex registers the skill under .agents/skills/metabolights-skill/SKILL.md.

What does metabolights-skill do?

It submits lightweight requests to MetaboLights endpoints and presents concise study-level metabolomics metadata in chat.

Are extra dependencies required to run the skill?

You only need a working Python environment to execute scripts/rest_request.py. The skill relies on no other runtime packages.

See also

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