skills.rest
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uniprot-database

Automate UniProt protein searches, sequence retrieval, and ID mapping via REST.

Updated Apr 19, 2026
Search Tags:#streaming#bioinformatics#rest-api#uniprot#id-mapping#sequence-retrieval#protein-search
One-click install
npx skills add https://github.com/CHENyiru3/AI-Skills-Collections --skill uniprot-database-chenyiru3
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: uniprot-database
Source: https://github.com/CHENyiru3/AI-Skills-Collections/tree/main/skills-market/compbio/multiomics/proteomics/uniprot
Command: npx skills add https://github.com/CHENyiru3/AI-Skills-Collections --skill uniprot-database-chenyiru3

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

UniProt offers programmatic access to protein data via REST, enabling automated searches, sequence retrieval, and cross-database mappings without manual web use.

Core Features & Use Cases

  • Search proteins by name, gene, organism, or accession with filters for review status.
  • Retrieve sequences (FASTA, etc.), fetch annotations, and perform ID mappings to Ensembl, RefSeq, PDB, and other databases.
  • Stream large result sets and perform batch queries to power analysis pipelines in reproducible research.

Quick Start

Use the UniProt REST API client to search human insulin proteins and retrieve sequences in FASTA format.

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 in FASTA format from UniProt using a REST API?▼

To retrieve protein sequences in FASTA format, use a REST API client to automate UniProt search queries by protein name, gene, or organism and fetch the sequence data directly via the endpoint.

What is the best way to batch query protein annotations and stream large result sets from UniProt?▼

Batch querying and streaming large result sets from UniProt is handled by applying REST API streaming techniques, enabling automated retrieval of extensive protein annotation data for reproducible research workflows.

Can I map protein accession IDs from UniProt to Ensembl, RefSeq, or PDB?▼

Cross-database ID mapping is fully supported, allowing you to map UniProt protein accession IDs directly to Ensembl, RefSeq, and PDB databases using the REST API.

Does the UniProt REST API return protein search results in JSON, TSV, and XML formats?▼

The UniProt REST API supports multiple data formats including JSON, TSV, and XML, allowing flexible integration of protein search results into various bioinformatics pipelines and analysis scripts.

How do I filter UniProt protein searches by review status and organism?▼

Filtering UniProt protein searches by review status and organism is accomplished through REST API query parameters, returning targeted protein annotations and sequences for specific bioinformatics applications.

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