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

This skill sends compact requests to the UniProt REST API and returns summaries for proteins, clusters, and sequences. Use it for focused bioinformatics lookups.

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

What uniprot-skill does

uniprot-skill lets an agent query the UniProt REST API through scripts/rest_request.py. It covers UniProtKB, UniRef, UniParc, and streaming FASTA requests. The default result is a compact summary; full JSON or FASTA is saved only when requested.

The script reads one JSON object from stdin. You can provide base_url, path, request parameters, response format, item limits, and a raw output path. Use uniprotkb/search for searches, uniprotkb/ for a single record, uniref/ for a cluster, and uniprotkb/stream for sequence output.

Install it when your agent needs repeatable UniProt lookups with concise chat results. Ask for machine-readable output when you need the complete JSON or FASTA payload.

What it helps with

  • search UniProtKB by gene and organism
  • retrieve a protein record by accession
  • summarize a UniRef cluster
  • stream protein sequences as FASTA

Example prompts for the agent

  • Search for `gene:TP53 AND organism_id:9606` and show accession and gene names.
  • Get JSON for `uniprotkb/P04637` and summarize the result.
  • Request two FASTA records for organism `562` through `uniprotkb/stream`.

How to install uniprot-skill

1Skills CLI (Vercel)

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

2Manually: put the files in place

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

For all projects use ~/.agents/skills/

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Questions about uniprot-skill

How do I install uniprot-skill in Codex?

Run npx skills add openai/plugins --skill uniprot-skill or npx skills add openai/plugins --skill uniprot-skill -a codex. The skill file is placed at .agents/skills/uniprot-skill/SKILL.md.

What does uniprot-skill do?

It sends compact UniProt REST API requests through scripts/rest_request.py and returns concise results for UniProtKB, UniRef, UniParc, and FASTA endpoints.

What is required to use the skill?

The skill relies on scripts/rest_request.py and reads JSON from stdin. For complete JSON or FASTA, request raw output with save_raw=true.

See also

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