Welcome to UniProtMapper’s documentation!

Contents:

UniProtMapper is a Python wrapper for UniProt’s Retrieve/ID Mapping RESTful API.

Main Features

  1. Map UniProt cross-referenced IDs to other identifiers & vice-versa

  2. Programmatically retrieve supported return and cross-reference fields (see Supported fields)

  3. Query UniProtKB entries using complex field-based queries (see Field Querying)

Quick Start

Installation:

pip install uniprot-id-mapper

Example 1. Use UniProtMapper to easily map between different protein identifiers:

from UniProtMapper import ProtMapper

mapper = ProtMapper()

result, failed = mapper.get(
    ids=["P30542", "Q16678", "Q02880"], from_db="UniProtKB_AC-ID", to_db="Ensembl"
)

Example 2. Programmatically retrieve fields from UniProtKB entries:

from UniProtMapper import ProtMapper

mapper = ProtMapper()

fields = ["accession", "gene_names", "organism_name"]
result, failed = mapper.get(
    ids=["P30542", "Q16678", "Q02880"], fields=fields
)

Example 3. Query UniProtKB entries using complex field-based queries:

from UniProtMapper import ProtKB
from UniProtMapper.uniprotkb_fields import (
    organism_name,
    length,
    reviewed,
    date_modified
)

# Find reviewed human proteins with length between 100-200 amino acids
# that were modified after January 1st, 2024
query = (
    organism_name("human") &
    reviewed(True) &
    length(100, 200) &
    date_modified("2024-01-01", "*")
)

protkb = ProtKB()
result = protkb.get(query)

Indices and tables