skills.rest
HolobiomicsLab
HolobiomicsLabOFFICIAL
Explore all skills by this author →
WebsiteGitHub

uniprot-database

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

4|1|Updated Jun 18, 2025
Search Tags:#bioinformatics#sequence#mapping#rest-api#protein#uniprot
One-click install
npx skills add https://github.com/HolobiomicsLab/Toolomics --skill uniprot-database-holobiomicslab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: uniprot-database
Source: https://github.com/HolobiomicsLab/Toolomics/tree/main/mcp_host/skills/scientific-skills/scientific-skills/uniprot-database
Command: npx skills add https://github.com/HolobiomicsLab/Toolomics --skill uniprot-database-holobiomicslab

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Direct REST API access to UniProt enables researchers and automation pipelines to perform protein searches, retrieve sequences, and map identifiers without manual web interaction.

Core Features & Use Cases

  • Programmatic search: query UniProt for proteins by name, gene, or accession.
  • Retrieve sequences and annotations: fetch FASTA/JSON data, access GO terms, domains, and functional notes.
  • ID mapping and cross-references: map UniProt IDs to external resources (PDB, Ensembl, RefSeq) and batch retrieve results.
  • Use Case: integrate protein lookups into a data analysis pipeline that compiles a FASTA sequence download and mapping results for a list of targets.

Quick Start

Run the UniProt client to search for a protein by name and retrieve its FASTA sequence.

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?▼

You can retrieve protein sequences from UniProt by querying the REST API to fetch FASTA or JSON data by name, gene, or accession. This supports direct sequence retrieval within Python workflows and data analysis pipelines.

How do I map UniProt IDs to external databases like PDB or Ensembl?▼

You can map UniProt IDs to external databases like PDB, Ensembl, and RefSeq using the UniProt ID mapping feature. It supports cross-database mapping operations, allowing batch retrieval of results for integration into analytical pipelines.

Can I batch retrieve protein annotations and stream large results from UniProt?▼

Yes, you can batch retrieve protein annotations and stream large results from UniProt. The REST API access supports batch operations, including streaming large datasets for GO terms, domains, and functional notes in Python.

What's the best way to perform programmatic protein searches without manual web interaction?▼

The best way to perform programmatic protein searches without manual web interaction is using UniProt REST API endpoints with a Python client. This allows automated querying for proteins by name, gene, or accession directly within data pipelines.

Does the UniProt REST API client require any specific dependencies for Python workflows?▼

Yes, the UniProt REST API client requires the requests dependency for Python workflows. It utilizes REST endpoints and a provided Python client in scripts/uniprot_client.py along with references for fields, mapping databases, and query syntax.

Related Skills

Explore More Data & Analytics Skills→
Runchuan-BURunchuan-BU
401

query-uniprot

Retrieve protein sequences and functional annotations from the UniProt REST API.

Community
Intermediate
biomaps-infrabiomaps-infra

db-uniprot

Query the UniProt REST API for protein searches, FASTA retrieval, and ID mapping.

Official
Intermediate
yf8578yf8578
1

gget

Query over 20 bioinformatics databases and perform sequence analysis via command-line or Python.

Community
Advanced
Yezez9Yezez9

gget

Query over 20 bioinformatics databases for gene and protein data.

Community
Advanced