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uniprot-database

Query UniProtKB, UniParc, and UniRef for protein metadata and sequences.

413|62|Updated Jun 23, 2026
Search Tags:#database#bioinformatics#genomics#sequence#protein#uniprot
One-click install
npx skills add https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit --skill uniprot-database-nvidia-bionemo
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: uniprot-database
Source: https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/plugins/bionemo-agent-toolkit/skills/complexa-binder-design/vendor/science-skills/uniprot_database
Command: npx skills add https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit --skill uniprot-database-nvidia-bionemo

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This skill solves the challenge of manually searching and retrieving accurate, curated biological data from massive protein databases, preventing errors and saving time in research workflows.

Core Features & Use Cases

  • Protein Discovery: Search UniProtKB, UniParc, and UniRef for functional annotations, sequences, and taxonomy.
  • Bulk Data Retrieval: Stream millions of entries efficiently for large-scale bioinformatics analysis.
  • ID Mapping: Convert identifiers between UniProt and over 100 external databases like Ensembl or PDB.

Quick Start

Use the uniprot-database skill to search for reviewed human proteins related to the p53 gene and return the first five results.

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 and functional annotations from UniProtKB?▼

You can retrieve protein sequences and functional annotations from UniProtKB by executing complex search queries and bulk streaming data via the UniProt REST and SPARQL APIs. This approach prevents manual search errors and saves research time.

What is the best way to map protein identifiers between UniProt and external databases?▼

The best way to map protein identifiers is using cross-database identifier mapping, which converts identifiers between UniProt and over 100 external databases like Ensembl or PDB for bioinformatics research.

Can I stream millions of protein entries for large-scale bioinformatics analysis?▼

Yes, you can stream millions of protein entries for large-scale bioinformatics analysis. The skill supports bulk data retrieval, allowing efficient streaming of massive entries from UniProtKB, UniParc, and UniRef databases.

Do I need specific Python libraries to access UniProt REST and SPARQL APIs?▼

Yes, you need standard Python libraries to interface with the UniProt REST and SPARQL APIs for reliable data extraction. No external dependencies are required to access UniProtKB, UniParc, and UniRef databases.

What limitations exist when querying UniParc and UniRef for protein metadata?▼

Limitations when querying UniParc and UniRef for protein metadata depend on the standard Python libraries interfacing with the UniProt REST and SPARQL APIs. Complex search queries must align with API rate limits and query syntax constraints.

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