skills.rest
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uniprot-database

Search UniProt entries and retrieve data via the REST API.

6|Updated Dec 30, 2025
Search Tags:#bioinformatics#mapping#rest-api#protein#uniprot#data-retrieval
One-click install
npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill uniprot-database-pur3v4d3r
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: uniprot-database
Source: https://github.com/pur3v4d3r/pur3-pkb-codebase/tree/main/.claude/skills/__scientific-skills/uniprot-database
Command: npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill uniprot-database-pur3v4d3r

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) and references (resource) components.

What problem does it solve?

The UniProt REST API skill provides direct programmatic access to UniProt entries, enabling fast searches, sequence retrieval, and cross-database ID mappings without manual browsing.

Core Features & Use Cases

  • Searching for proteins by name, gene, organism, or accession
  • Retrieving protein sequences in FASTA or other formats
  • Batch retrieval and ID mapping across databases (Ensembl, RefSeq, PDB, GO, etc.)
  • Streaming large result sets and customizing retrieved fields for efficient data transfer
  • Python client scripts (scripts/uniprot_client.py) to simplify common workflows

Quick Start

Query UniProt for a protein entry and retrieve its data with the included Python client.

Frequently Asked Questions about uniprot-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I retrieve protein sequences from UniProt using a REST API?▼

Batch retrieval from UniProt is supported by submitting multiple accessions to the REST API. The Skill handles rate limits automatically and uses streaming to efficiently transfer large protein datasets.

How do I map protein IDs across databases like Ensembl and RefSeq?▼

Cross-database ID mapping translates identifiers between UniProt and databases like Ensembl, RefSeq, or PDB. The Skill sends validated requests to the REST API and returns the mapped entries in JSON format.

Do I need Python and the requests library to query the UniProt database?▼

Yes, you need Python with the requests library installed. The Skill provides Python client scripts that simplify query workflows, manage input validation, and handle REST API connections for data retrieval.

What is the best way to handle rate limits when streaming large UniProt datasets?▼

To handle rate limits when streaming large UniProt datasets, use a REST API approach that manages request throttling. The Skill automatically enforces rate limits and processes large query results via streaming.

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