uniprot-id-mapper

UniProtMapper

Easily retrieve UniProt data and map protein identifiers using this Python package for UniProt's Retrieve & ID Mapping RESTful APIs. Read the full documentation.

📚 Table of Contents

• ⛏️ Features
• 📦 Installation
• 🛠️ Usage
  • Mapping IDs
  • Retrieving Information
  • Field-based Querying
• 📖 Documentation
• 💻 Command Line Interface (CLI)
• 👏🏼 Credits

⛏️ Features

UniProtMapper is a tool for bioinformatics and proteomics research that supports:

• Mapping any UniProt cross-referenced IDs to other identifiers & vice-versa;
• Programmatically retrieving any of the supported return and cross-reference fields from both UniProt-SwissProt and UniProt-TrEMBL (unreviewed) databases. For a full table containing all the supported resources, refer to the supported fields in the docs;
• Querying UniProtKB entries using complex field-based queries with boolean operators ~ (NOT), | (OR), & (AND).

For the first two functionalities, check the examples Mapping IDs and Retrieving Information below. The third, see Field-based Querying.

The ID mapping API can also be accessed through the CLI. For more information, check CLI.

📦 Installation

From PyPI (recommended):

python -m pip install uniprot-id-mapper

Directly from GitHub:

python -m pip install git+https://github.com/David-Araripe/UniProtMapper.git

From source:

git clone https://github.com/David-Araripe/UniProtMapper
cd UniProtMapper
python -m pip install .

🛠️ Usage

Mapping IDs

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"
)

The result is a pandas DataFrame containing the mapped IDs (see below), while failed is a list of identifiers that couldn't be mapped.

	UniProtKB_AC-ID	Ensembl
0	P30542	ENSG00000163485.17
1	Q16678	ENSG00000138061.12
2	Q02880	ENSG00000077097.17

Retrieving Information

A DataFrame with the supported return fields is accessible through the attribute ProtMapper.fields_table:

from UniProtMapper import ProtMapper

mapper = ProtMapper()
df = mapper.fields_table
df.head()

	label	returned_field	field_type	has_full_version	type
0	Entry	accession	Names & Taxonomy	-	uniprot_field
1	Entry Name	id	Names & Taxonomy	-	uniprot_field
2	Gene Names	gene_names	Names & Taxonomy	-	uniprot_field
3	Gene Names (primary)	gene_primary	Names & Taxonomy	-	uniprot_field
4	Gene Names (synonym)	gene_synonym	Names & Taxonomy	-	uniprot_field

From the DataFrame, all return_field entries can be used to access UniProt data programmatically:

# To retrieve the default fields:
result, failed = mapper.get(["Q02880"])
>>> Fetched: 1 / 1

# Retrieve custom fields:
fields = ["accession", "organism_name", "structure_3d"]
result, failed = mapper.get(["Q02880"], fields=fields)
>>> Fetched: 1 / 1

Further, for the cross-referenced fields that have has_full_version set to yes, returning the same field with extra information is supported by passing <field_name>_full, such as xref_pdb_full.

All available return fields are also accessible through the attribute ProtMapper.supported_return_fields:

from UniProtMapper import ProtMapper
mapper = ProtMapper()
print(mapper.supported_return_fields)

>>> ['accession',
>>>  'id',
>>>  'gene_names',
>>>  ...
>>>  'xref_smart_full',
>>>  'xref_supfam_full']

Field-based Querying

UniProtMapper supports complex field-based protein queries using boolean operators (AND, OR, NOT) through the uniprotkb_fields module. This allows you to create sophisticated searches combining multiple criteria. For example:

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)

For a list of all fields and their descriptions, check the API reference for the uniprotkb_fields module reference.

📖 Documentation

• Stable Branch Documentation (master branch)
• Development Documentation (dev branch)

💻 Command Line Interface (CLI)

UniProtMapper provides a CLI for the ID Mapping class, ProtMapper, for easy access to lookups and data retrieval. Here is a list of the available arguments, shown by protmap -h:

usage: UniProtMapper [-h] -i [IDS ...] [-r [RETURN_FIELDS ...]] [--default-fields] [-o OUTPUT]
                     [-from FROM_DB] [-to TO_DB] [-over] [-pf]

Retrieve data from UniProt using UniProt's RESTful API. For a list of all available fields, see: https://www.uniprot.org/help/return_fields 

Alternatively, use the --print-fields argument to print the available fields and exit the program.

optional arguments:
  -h, --help            show this help message and exit
  -i [IDS ...], --ids [IDS ...]
                        List of UniProt IDs to retrieve information from. Values must be
                        separated by spaces.
  -r [RETURN_FIELDS ...], --return-fields [RETURN_FIELDS ...]
                        If not defined, will pass `None`, returning all available fields.
                        Else, values should be fields to be returned separated by spaces. See
                        --print-fields for available options.
  --default-fields, -def
                        This option will override the --return-fields option. Returns only the
                        default fields stored in: <pkg_path>/resources/cli_return_fields.txt
  -o OUTPUT, --output OUTPUT
                        Path to the output file to write the returned fields. If not provided,
                        will write to stdout.
  -from FROM_DB, --from-db FROM_DB
                        The database from which the IDs are. For the available cross
                        references, see: <pkg_path>/resources/uniprot_mapping_dbs.json
  -to TO_DB, --to-db TO_DB
                        The database to which the IDs will be mapped. For the available cross
                        references, see: <pkg_path>/resources/uniprot_mapping_dbs.json
  -over, --overwrite    If desired to overwrite an existing file when using -o/--output
  -pf, --print-fields   Prints the available return fields and exits the program.

Usage example, retrieving default fields from <pkg_path>/resources/cli_return_fields.txt:

👏🏼 Credits

• UniProt for providing the API and the amazing database;
• Andrew White and the University of Rochester for the protein emoji;

For issues, feature requests, or questions, please open an issue on the GitHub repository.