bio-uniprot-access

Version Compatibility

Reference examples tested with: BioPython 1.83+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

UniProt Access

Query UniProt for protein sequences, functional annotations, and cross-references.

"Get protein information from UniProt" → Fetch sequences, GO terms, domains, and cross-references for a protein accession.

• Python: requests.get(f'https://rest.uniprot.org/uniprotkb/{acc}.json') (UniProt REST API)
• Python: ExPASy.get_sprot_raw(acc) + SwissProt.read() (BioPython)

UniProt REST API

Fetch Single Entry

import requests

def fetch_uniprot(accession, format='fasta'):
    '''Fetch UniProt entry. Formats: fasta, json, txt, xml, gff'''
    url = f'https://rest.uniprot.org/uniprotkb/{accession}.{format}'
    response = requests.get(url)
    response.raise_for_status()
    return response.text

sequence = fetch_uniprot('P53_HUMAN', 'fasta')
entry_json = fetch_uniprot('P04637', 'json')

Search UniProt

Goal: Find UniProt protein entries matching gene name, organism, or functional criteria.

Approach: Query the UniProt REST search endpoint with structured query syntax and parse the JSON results for accessions and protein descriptions.

def search_uniprot(query, format='json', size=25):
    '''Search UniProt with query syntax'''
    url = 'https://rest.uniprot.org/uniprotkb/search'
    params = {'query': query, 'format': format, 'size': size}
    response = requests.get(url, params=params)
    response.raise_for_status()
    return response.json() if format == 'json' else response.text

results = search_uniprot('gene:BRCA1 AND organism_id:9606')
for entry in results['results']:
    print(entry['primaryAccession'], entry['proteinDescription']['recommendedName']['fullName']['value'])