medsci-agent: Skill for OpenCode

UniProt Protein Database

Overview

UniProt is the comprehensive resource for protein sequence and functional annotation. UniProtKB has two sections: Swiss-Prot (reviewed, curated) and TrEMBL (unreviewed, automated).

REST API Access

import requests

# Fetch a single entry
r = requests.get("https://rest.uniprot.org/uniprotkb/P04637.json")
entry = r.json()
print(entry["proteinDescription"]["recommendedName"]["fullName"]["value"])

Search Queries

params = {
    "query": "(gene:TP53) AND (organism_id:9606) AND (reviewed:true)",
    "format": "json",
    "size": 10,
    "fields": "accession,gene_names,protein_name,organism_name,length"
}
r = requests.get("https://rest.uniprot.org/uniprotkb/search", params=params)
results = r.json()["results"]

Key Fields

• accession: Primary identifier (e.g., P04637 for human TP53).
• gene_names: Associated gene symbols.
• features: Domains, active sites, variants, PTMs.
• cross-references: Links to PDB, Pfam, GO, ChEMBL, etc.
• sequence: Full amino acid sequence.

Common Query Syntax

• gene:BRCA1 -- by gene name.
• organism_id:9606 -- human.
• reviewed:true -- Swiss-Prot only.
• ec:3.4.21.* -- by enzyme classification.
• keyword:kinase -- by keyword annotation.

Key Details

• Accession format: [OPQ][0-9][A-Z0-9]{3}[0-9] (e.g., P04637).
• Batch retrieval: POST to /uniprotkb/accessions with list of IDs.
• ID mapping: https://rest.uniprot.org/idmapping/run for cross-database mapping.