Can I filter specifically for reviewed protein entries?

Yes, you can specifically target the Swiss-Prot (manually curated) database by adding the 'reviewed:true' filter to your search queries for higher data quality.

What data can I retrieve from UniProt with this skill?

You can access amino acid sequences (FASTA), gene names, functional annotations, GO terms, domain information, and cross-references to thousands of other biological databases.

How does the ID mapping feature work?

The ID mapping feature allows you to submit lists of identifiers from external databases like Ensembl or RefSeq and convert them into UniProt accessions for consolidated analysis.

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

Standard queries use pagination, but for large-scale data collection, the skill provides access to the streaming endpoint which can handle batch retrieval of up to 100,000 identifiers.

UniProt Protein Database

Name: UniProt Protein Database
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Accesses the UniProt REST API to retrieve protein sequences, functional annotations, and map identifiers across biological databases.

This skill integrates Claude with the UniProt Knowledgebase, the world's leading resource for protein sequence and functional information. It enables users to perform complex searches by gene, accession, or organism, retrieve high-quality protein data in multiple formats like FASTA and JSON, and perform large-scale ID mapping across external databases like Ensembl, RefSeq, and PDB. This is an essential tool for bioinformaticians and life science researchers who require direct, programmatic control over protein data retrieval and analysis workflows within their coding environment.

Key Features

01Comprehensive protein search by gene, name, accession, or taxonomy

02Stream large result sets for high-throughput protein data analysis

030 GitHub stars

04Access detailed functional annotations, GO terms, and protein domains

05Retrieve sequences in FASTA, JSON, XML, and TSV formats

06Cross-database identifier mapping for Ensembl, RefSeq, PDB, and more

Use Cases

01Mapping biological identifiers between UniProt and external research databases

02Automated retrieval of amino acid sequences for specific gene lists

03Filtering and downloading curated Swiss-Prot protein data for bioinformatic pipelines

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos uniprot-database

For use in Claude.ai and ChatGPT

Download Skill