uniprot-database

Query UniProt REST API for protein search, sequence retrieval, and identifier mapping.

52|6|Updated Nov 24, 2025

Search Tags:#REST #UniProt #sequence #protein

Ready to run

npx skills add https://github.com/ovachiever/droid-tings --skill uniprot-database-ovachiever

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: uniprot-database
Source: https://github.com/ovachiever/droid-tings/tree/main/skills/uniprot-database
Command: npx skills add https://github.com/ovachiever/droid-tings --skill uniprot-database-ovachiever

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Retrieve protein sequences and annotations from UniProt via REST API.

Core Features & Use Cases

Search by name, gene, accession and organism
Retrieve sequences in FASTA or other formats
ID mapping across databases
GO terms and annotations for proteins

Quick Start

Quick start: search by gene and fetch GO terms.

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 via REST API?▼

UniProt REST API provides direct programmatic access to protein sequences in multiple formats including FASTA, JSON, TSV, XML, and RDF. Query by protein name, gene symbol, accession identifier, or organism; retrieve sequences and annotations through REST endpoints with field filtering and pagination support for automated workflows.

Can I search UniProt by gene name or accession number programmatically?▼

Yes, the UniProt REST API supports searches by gene name, accession number, protein name, and organism filter. Results return in your chosen format with configurable field selection, enabling batch lookups and automated protein identification across large datasets.

What's the best way to map protein identifiers across different databases?▼

UniProt ID mapping via REST API converts protein identifiers between UniProt accessions and external database formats. Submit batch requests with up to 100,000 IDs; results remain accessible for 7 days, enabling large-scale cross-database reconciliation in programmatic workflows.

How do I retrieve GO terms and functional annotations for proteins?▼

Query the UniProt REST API with protein accessions or search terms to retrieve GO terms, functional annotations, and structured metadata. Use field filtering to extract specific annotation types and format results as JSON, TSV, or XML for downstream analysis.

Does UniProt REST API support streaming large protein datasets?▼

Yes, the UniProt REST API supports pagination and streaming of large datasets with batch constraints of 100,000 IDs maximum per job. Results persist for 7 days, enabling retrieval and processing of genome-scale protein collections through automated REST queries.

What formats does UniProt REST API return for protein sequence data?▼

UniProt REST API delivers sequences and annotations in JSON, TSV, FASTA, XML, and RDF formats. Select formats based on downstream tool compatibility; use field parameters to include only required data fields and reduce response size in automated pipelines.