Bio2BEL WikiPathways

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.

If you find this package useful, please consider citing [domingofernandez2018]:

[domingofernandez2018]

Domingo-Fernandez, D., et al (2018). ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases. Npj Systems Biology and Applications, __5__(1), 3.

Warning This package creates partOf relationships in BEL, but does not convert WikiPathways mechanistic relationships to BEL. That functionality is implemented in the PathMe project.

Installation

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

$ pip install bio2bel_wikipathways

or from the latest code on GitHub in development mode with:

$ git clone https://github.com/bio2bel/wikipathways.git
$ cd wikipathways
$ pip install -e .

Setup

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

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 bio2bel_wikipathways web (http://localhost:5000/admin/)
• Export gene sets for programmatic use 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