What is the UniProt Database skill?

It is a specialized capability for Claude that allows for direct programmatic interaction with the UniProt REST API to search, retrieve, and analyze protein data.

Is there a limit to how many proteins I can retrieve?

While standard searches have pagination limits, this skill includes support for the UniProt stream endpoint to handle very large datasets efficiently.

Can I use this for bulk ID mapping?

Yes, the skill supports mapping identifiers between UniProt and various external databases like Ensembl, RefSeq, and PDB for up to 100,000 IDs per job.

What file formats are supported for sequence retrieval?

The skill supports retrieving protein data in several formats including JSON, TSV, FASTA, XML, and Excel, depending on your workflow needs.

Does it distinguish between reviewed and unreviewed data?

Yes, you can use the search syntax to specifically target reviewed (Swiss-Prot) entries for higher data quality or unreviewed (TrEMBL) entries for broader coverage.

UniProt Database Integration

Name: UniProt Database Integration
Author: ricable

byricable

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Data Science & ML

Enables direct REST API access to UniProt for protein searching, FASTA sequence retrieval, and cross-database identifier mapping.

This skill provides a specialized interface for Claude to interact with the UniProt protein sequence and functional information resource, allowing developers and researchers to automate complex bioinformatics workflows. It simplifies tasks such as searching for protein entries by gene symbol or accession, retrieving sequences for analysis, mapping identifiers between major databases like Ensembl and PDB, and accessing detailed functional annotations from both curated Swiss-Prot and computer-annotated TrEMBL datasets. By providing standardized access to the UniProt REST API, it bridges the gap between AI coding assistants and the world's leading protein knowledgebase.

Key Features

01Automated ID mapping between UniProt and over 40 external databases

02Support for streaming large datasets and customizing specific data fields

03Access to detailed functional annotations, GO terms, and protein domains

04Bulk retrieval of protein sequences in FASTA, JSON, and TSV formats

051 GitHub stars

06Advanced protein search using natural language or structured boolean syntax

Use Cases

01Automating the retrieval of protein sequences for structural biology and folding pipelines

02Programmatically querying protein functional annotations to enrich experimental datasets

03Mapping large lists of gene identifiers to UniProt accessions for multi-omic data integration

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add ricable/ultimate-ai-agent uniprot-database

For use in Claude.ai and ChatGPT

Download Skill