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uniprot-database

Access UniProt REST API for protein search, retrieval, and ID mapping.

21|1|Updated Mar 19, 2026
Search Tags:#bioinformatics#rest-api#uniprot#id-mapping#fasta#protein-search#python-client
One-click install
npx skills add https://github.com/OwnLabAI/ownlab --skill uniprot-database-ownlabai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: uniprot-database
Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/uniprot-database
Command: npx skills add https://github.com/OwnLabAI/ownlab --skill uniprot-database-ownlabai

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Direct programmatic access to the UniProt REST API enables researchers and developers to perform protein searches, sequence retrieval, and ID mapping without manual browser interactions.

Core Features & Use Cases

  • Search proteins by name, gene, accession, or organism using the REST endpoints.
  • Retrieve protein sequences and annotations in FASTA, JSON, TSV, or other supported formats.
  • Map identifiers across databases (e.g., UniProt to PDB, Ensembl, RefSeq) using the idmapping endpoints.
  • Use the included Python client to automate workflows, batch queries, and streaming retrieval.

Quick Start

Install dependencies and run the UniProt REST client to search proteins, retrieve sequences, and map IDs.

Frequently Asked Questions about uniprot-database

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

FAQPage Schema
How do I search and retrieve protein sequences from UniProt programmatically?▼

You can search and retrieve protein sequences from UniProt programmatically by accessing the /uniprotkb/search and /uniprotkb/{accession}.{format} REST endpoints, supporting FASTA, JSON, and TSV outputs.

Can I map protein identifiers across different databases like Ensembl and PDB?▼

Yes, you can map protein identifiers across databases like Ensembl and PDB using the UniProt /idmapping/run endpoint, which supports batch mapping to convert IDs between different biological databases.

What is the best way to handle large protein search results from the UniProt REST API?▼

The best way to handle large protein search results is by using the UniProt /uniprotkb/stream endpoint, which allows streaming large query outputs efficiently without hitting standard pagination limits.

Do I need Python and the requests library to use this UniProt API client?▼

Yes, you need Python and the requests library installed to use this UniProt API client, which provides a Python interface and example scripts to automate workflows, batch queries, and sequence retrieval.

Does the UniProt REST API support field customization for protein search queries?▼

Yes, the UniProt REST API supports field customization for protein search queries, allowing you to tailor the returned data fields when searching or streaming results from the UniProtKB database.

Can I run batch ID mapping workflows for multiple proteins simultaneously?▼

Yes, you can run batch ID mapping workflows for multiple proteins simultaneously by utilizing the /idmapping/run endpoint combined with the included Python client to automate and streamline the conversion process.

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