bio2bel-expasy 0.2.0

A package for parsing and storing the ExPASy Enzyme Database

This repository downloads and parses the enzyme classes from the ExPASy ENZYME database

Installation

bio2bel_expasy can be installed easily from PyPI with the following code in your favorite terminal:

$ python3 -m pip install bio2bel_expasy

or from the latest code on GitHub with:

$ python3 -m pip install git+https://github.com/bio2bel/expasy.git@master

or check the installation instructions.

Setup

ExPASy can be downloaded and populated from either the Python REPL or the automatically installed command line utility.

Python REPL

>>> import bio2bel_expasy
>>> expasy_manager = bio2bel_expasy.Manager()
>>> expasy_manager.populate()

Command Line Utility

bio2bel_expasy populate

Programmatic Interface

To enrich the proteins in a BEL Graph with their enzyme classes, use:

>>> from bio2bel_expasy import enrich_proteins
>>> graph = ... # get a BEL graph
>>> enrich_proteins(graph)

Citations

Gasteiger, E., et al. (2003). ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 31(13), 3784–8.