bio2bel-kegg 0.2.1

A wraper around the KEGG RESTful API

This package allows the enrichment of BEL networks with KEGG information by wrapping its RESTful API. Furthermore, it is integrated in the ComPath environment for pathway database comparison.

Installation

bio2bel_kegg can be installed easily from PyPI with the following code in your favorite terminal:

$ python3 -m pip install bio2bel_kegg

or from the latest code on GitHub with:

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

Setup

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

The following resources will be automatically installed and loaded in order to fully populate the tables of the database:

• Bio2BEL HGNC

Python REPL

>>> import bio2bel_kegg
>>> kegg_manager = bio2bel_kegg.Manager()
>>> kegg_manager.populate()

Command Line Utility

bio2bel_kegg populate

Other Command Line Utilities

• Run an admin site for simple querying and exploration python3 -m bio2bel_kegg web (http://localhost:5000/admin/)

• Export gene sets for programmatic use python3 -m bio2bel_kegg export

Citation

• Kanehisa, Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K.; KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353-D361 (2017).

• Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016).

• Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).