skills.rest
JosephWoodall
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uniprot-database

Search, retrieve, and map UniProt protein data via REST API.

1|Updated Mar 19, 2026
Search Tags:#api#python#rest#mapping#client#protein#uniprot
One-click install
npx skills add https://github.com/JosephWoodall/noosphere --skill uniprot-database-josephwoodall
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: uniprot-database
Source: https://github.com/JosephWoodall/noosphere/tree/main/.agent/skills/uniprot-database
Command: npx skills add https://github.com/JosephWoodall/noosphere --skill uniprot-database-josephwoodall

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 programmatic protein searches, sequence retrieval, and ID mapping without manual web interactions.

Core Features & Use Cases

  • Search UniProt entries by name, gene, accession, or organism and retrieve results in JSON, TSV, FASTA, or other formats.
  • Retrieve individual protein entries or perform batch retrieval and ID mappings via the UniProt API.
  • Use the provided Python client (scripts/uniprot_client.py) to integrate UniProt into automated pipelines and analyses.

Quick Start

Run a basic search using the Python client to fetch human insulin data in JSON 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 from UniProt using a Python REST API client?▼

You can retrieve protein sequences from UniProt by using a Python REST API client to query search endpoints and return data in formats like JSON, TSV, or FASTA for automated pipelines.

What is the best way to perform batch ID mapping for UniProt entries?▼

Batch ID mapping for UniProt entries is handled by sending programmatic REST API requests, allowing you to map multiple protein identifiers across different databases within your Python workflows.

Can I search UniProt entries by organism and gene name in a data pipeline?▼

Yes, you can search UniProt entries by organism, gene name, or accession through REST endpoints, integrating the queries directly into your data pipelines for automated batch processing.

Does the UniProt REST API support streaming queries for large protein datasets?▼

The UniProt REST API supports stream queries, enabling you to efficiently process and retrieve large protein datasets directly through the Python client without manual web interactions.

Do I need the requests library to run a UniProt Python client?▼

Yes, you need the requests library installed in your Python environment, as it is the required dependency for executing the REST queries and mapping functions within the UniProt client.

How do I configure UniProt REST queries to return specific protein fields?▼

You can configure UniProt REST queries to return specific protein fields by utilizing the field and config endpoints provided by the API, ensuring your Python client retrieves only necessary data.

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