Agent skill · research science · davila7
uniprot-database
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.
Why this skill is useful
Provides specific REST API commands and workflows for protein data retrieval that the AI wouldn't reliably generate on its own.
What it needs
About 3k tokens when loaded. Last updated 2026-08-06. 30,138 stars on the source repository.
What this skill does
UniProt Database Overview UniProt is the world's leading comprehensive protein sequence and functional information resource. Search proteins by name, gene, or accession, retrieve sequences in FASTA format, perform ID mapping across databases, access Swiss-Prot/TrEMBL annotations via REST API for protein analysis. When to Use This Skill This skill should be used when: Searching for protein entries by name, gene symbol, accession, or organism Retrieving protein sequences in FASTA or other formats Mapping identifiers between UniProt and external databases (Ensembl, RefSeq, PDB, etc.) Accessing protein annotations including GO terms, domains, and functional descriptions Batch retrieving multiple protein entries efficiently Querying reviewed (Swiss-Prot) vs. unreviewed (TrEMBL) protein data Streaming large protein datasets Building custom queries with field-specific search syntax Core Capabilities 1. Searching for Proteins Search UniProt using natural language queries or structured search syntax. Common search patterns: Use the API search endpoint: https://rest.uniprot.org/uniprotkb/search?query={query}&format={format} Supported formats: JSON, TSV, Excel, XML, FASTA, RDF, TXT 2. Retrieving Individual Protein Entries Retrieve specific protein entries by accession number. Accession number formats: Classic: P12345, Q1AAA9, O15530 (6 characters: letter + 5 alphanumeric) Extended: A0A022YWF9 (10 characters for newer entries) Retrieve endpoint: https://rest.uniprot.org/uniprotkb/{accession}.{format} Example: https://rest.uniprot.org/uniprotkb/P12345.fasta 3. Batch Retrieval and ID Mapping Map protein identifiers between different database systems and retrieve multiple entries efficiently. ID Mapping workflow: 1. Submit mapping job to: https://rest.uniprot.org/idmapping/run 2. Check job status: https://rest.uniprot.org/idmapping/status/{jobId} 3. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills davila7/uniprot-database