Bio2BEL KEGG

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).

Metadata

Release files for bio2bel-kegg 0.2.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for bio2bel-kegg 0.2.1
File	Size	Uploaded
bio2bel_kegg-0.2.1.tar.gz	29.9 kB	Nov 13, 2018	Details

Built distribution (wheel)

Table of built distributions (wheels) for bio2bel-kegg 0.2.1
File	Interpreter	ABI	Platform	Reset
bio2bel_kegg-0.2.1-py3-none-any.whl 15.0 kB Nov 13, 2018	Python 3	none	any	Details

Total release size: 45.0 kB

Release files / bio2bel_kegg-0.2.1.tar.gz

Download URL	bio2bel_kegg-0.2.1.tar.gz
Size	29.9 kB
Tags	Source
SHA-256 checksum How to use checksums	`4fd90d5bb179d93610f394f96ebe6d897346d041e67cc66837af4f897bdee301`
BLAKE2b-256 checksum How to use checksums	`39de2bede7de4519e728cdc2f920d8bde718daad393d5462702bd6ec12c1d77d`
Upload date	Nov 13, 2018
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/1.12.1 pkginfo/1.4.2 requests/2.20.1 setuptools/40.6.2 requests-toolbelt/0.8.0 tqdm/4.28.1 CPython/3.7.0`

Release files / bio2bel_kegg-0.2.1-py3-none-any.whl

Download URL	bio2bel_kegg-0.2.1-py3-none-any.whl
Size	15.0 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`45934c853032404a47e39fea2162ba05fb29cc6923941c186135e64d3029eb2c`
BLAKE2b-256 checksum How to use checksums	`7b3712281db0dabd22d94f3b8f4af9a6047e20b3f30f001cf0985f3ab5fd5466`
Upload date	Nov 13, 2018
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/1.12.1 pkginfo/1.4.2 requests/2.20.1 setuptools/40.6.2 requests-toolbelt/0.8.0 tqdm/4.28.1 CPython/3.7.0`