bio2bel-wikipathways

A package for converting Wikipathways to BEL

Project description

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

Installation

bio2bel_wikipathways can be installed easily from PyPI with the following code in your favorite terminal:

$ python3 -m pip install bio2bel_wikipathways

or from the latest code on GitHub with:

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

Setup

WikiPathways 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_wikipathways
>>> wikipathways_manager = bio2bel_wikipathways.Manager()
>>> wikipathways_manager.populate()

Command Line Utility

bio2bel_wikipathways populate

Other Command Line Utilities

Run an admin site for simple querying and exploration python3 -m bio2bel_wikipathways web (http://localhost:5000/admin/)
Export gene sets for programmatic use python3 -m bio2bel_wikipathways export

Citation

Slenter, D.N., et al WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research Nucleic Acids Research, (2017) doi.org/10.1093/nar/gkx1064
Kutmon, M., et al. WikiPathways: capturing the full diversity of pathway knowledge Nucl. Acids Res., 44, D488-D494 (2016) doi:10.1093/nar/gkv1024
Kelder, T., et al. WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 2012 Jan;40(Database issue):D1301-7

Project details

Release history Release notifications | RSS feed

0.2.3

Mar 13, 2019

0.2.2

Jan 14, 2019

0.2.1

Jan 11, 2019

0.2.0

Nov 13, 2018

0.1.4

Oct 13, 2018

0.1.3

Oct 13, 2018

0.1.2

Jul 31, 2018

0.1.2.dev0 pre-release

Jul 31, 2018

0.1.1

Jul 31, 2018

0.1.1.dev0 pre-release

Jul 31, 2018

0.1.0

Jul 31, 2018

0.1.0.dev0 pre-release

Jul 31, 2018

0.0.12

Jul 26, 2018

This version

0.0.11

Jun 1, 2018

0.0.11.dev0 pre-release

Jun 1, 2018

0.0.10

Jun 1, 2018

0.0.10.dev0 pre-release

Jun 1, 2018

0.0.9

Jun 1, 2018

0.0.9.dev0 pre-release

Jun 1, 2018

0.0.8

May 11, 2018

0.0.7

May 4, 2018

0.0.6

Apr 24, 2018

0.0.5

Apr 18, 2018

0.0.4

Apr 18, 2018

0.0.3

Mar 23, 2018

0.0.2

Mar 2, 2018

0.0.1

Feb 14, 2018

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