bio2bel-wikipathways 0.2.3

Description:

bio2belwikipathways 0.2.3

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