/uniprot-protein-database

name: uniprot-protein-database
description: "Query UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations. Use bioservices for multi-DB access; alphafold-database-access for structures."
license: CC-BY-4.0

UniProt — Protein Database

Overview

UniProt is the most comprehensive protein sequence and functional annotation database, containing 250M+ entries. This skill covers programmatic access via the UniProt REST API for protein search, sequence retrieval, ID mapping, and annotation queries. Swiss-Prot entries are manually curated; TrEMBL entries are computationally predicted.

When to Use

• Searching for proteins by gene name, accession, organism, or function keywords
• Retrieving protein sequences in FASTA format for downstream analysis
• Mapping identifiers between databases (UniProt ↔ Ensembl, PDB, RefSeq, KEGG)
• Accessing protein annotations: GO terms, domains, post-translational modifications
• Batch retrieving multiple protein entries for comparative analysis
• Downloading reviewed (Swiss-Prot) protein datasets for a specific organism
• For **unified access to 40+ databases**, use bioservices instead
• For **protein 3D structures**, use alphafold-database-access or pdb-database

Prerequisites

pip install requests pandas

**API Rate Limits**: UniProt REST API has no strict rate limit but recommends adding `time.sleep(0.5)` between batch requests. For large queries (>10k results), use the streaming endpoint instead of paginated search. Maximum 100,000 IDs per ID mapping job.

Quick Start

import requests

# Search for human insulin proteins (reviewed/Swiss-Prot only)
url = "https://rest.uniprot.org/uniprotkb/search"
params = {"query": "insulin AND organism_id:9606 AND reviewed:true", "format": "tsv",
          "fields": "accession,gene_names,protein_name,length"}
response = requests.get(url, params=params)
print(response.text[:500])
# accession  gene_names  protein_name  length
# P01308     INS         Insulin       110

Core API

1. Protein Search

Search UniProt with structured queries combining Boolean operators and field-specific filters.

import requests
import time

BASE = "https://rest.uniprot.org/uniprotkb/search"

def search_uniprot(query, fields=None, format="json", size=25):
    """Search UniProt with query syntax."""
    params = {"query": query, "format": format, "size": size}
    if fields:
        params["fields"] = ",".join(fields)
    resp = requests.get(BASE, params=params)
    resp.raise_for_status()
    return resp.json() if format == "json" else resp.text

# Search by gene name
results = search_uniprot("gene:BRCA1 AND reviewed:true",
                         fields=["accession", "gene_names", "organism_name", "length"])
for entry in results["results"][:3]:
    print(f"{entry['primaryAccession']} | {entry.get('genes', [{}])[0].get('geneName', {}).get('value', 'N/A')} | {entry.get('organism', {}).get('scientificName', 'N/A')}")

**Query syntax reference**:

# Boolean operators
kinase AND organism_id:9606          # Human kinases
(diabetes OR insulin) AND reviewed:true
cancer NOT lung

# Field-specific
gene:BRCA1
accession:P12345
taxonomy_name:"Homo sapiens"
go:0005515                           # GO term: protein binding

# Range queries
length:[100 TO 500]
mass:[50000 TO 100000]

# Wildcards
gene:BRCA*

2. Protein Entry Retrieval

Retrieve individual protein entries by accession number.

import requests

def get_protein(accession, format="json"):
    """Retrieve a single protein entry."""
    url = f"https://rest.uniprot.org/uniprotkb/{accession}"
    resp = requests.get(url, headers={"Accept": f"application/{format}"})
    resp.raise_for_status()
    return resp.json() if format == "json" else resp.text

# Get human insulin
entry = get_protein("P01308")
print(f"Protein: {entry['proteinDescription']['recommendedName']['fullName']['value']}")
print(f"Gene: {entry['genes'][0]['geneName']['value']}")
print(f"Length: {entry['sequence']['length']} aa")
print(f"Sequence: {entry['sequence']['value'][:50]}...")

# Get FASTA directly
fasta = requests.get("https://rest.uniprot.org/uniprotkb/P01308.fasta").text
print(fasta[:200])

3. ID Mapping

Map identifiers between UniProt and other databases.

import requests
import time

def map_ids(ids, from_db, to_db):
    """Map identifiers between databases (async job)."""
    # Submit job
    resp = requests.post("https://rest.uniprot.org/idmapping/run",
                         data={"from": from_db, "to": to_db, "ids": ",".join(ids)})
    resp.raise_for_status()
    job_id = resp.json()["jobId"]

    # Poll for completion
    while True:
        status = requests.get(f"https://rest.uniprot.org/idmapping/status/{job_id}").json()
        if "results" in status or "failedIds" in status:
            break
        time.sleep(1)

    # Get results
    results = requests.get(f"https://rest.uniprot.org/idmapping/results/{job_id}").json()
    return results

# UniProt → PDB mapping
results = map_ids(["P01308", "P12345"], from_db="UniProtKB_AC-ID", to_db="PDB")
for r in results.get("results", []):
    print(f"{r['from']} → PDB: {r['to']}")

# UniProt → Ensembl mapping
results = map_ids(["P01308"], from_db="UniProtKB_AC-ID", to_db="Ensembl")
for r in results.get("results", []):
    print(f"{r['from']} → Ensembl: {r['to']}")

**Common database codes**: `UniProtKB_AC-ID`, `Ensembl`, `RefSeq_Protein`, `PDB`, `Gene_Name`, `GeneID`, `KEGG`

4. Batch Retrieval and Streaming

Retrieve large datasets efficiently.

import requests
import time

def batch_retrieve(accessions, fields=None, format="tsv"):
    """Retrieve multiple proteins by accession."""
    query = " OR ".join(f"accession:{acc}" for acc in accessions)
    params = {"query": query, "format": format}
    if fields:
        params["fields"] = ",".join(fields)
    resp = requests.get("https://re