bio2bel-wikipathways 0.0.5

A package for converting Wikipathways to BEL

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

This code can be installed with pip3 install git+https://github.com/bio2bel/wikipathways.git

Note that the Bio2BEL HGNC should be installed and loaded in order to map ENTREZ identifiers to HGNC Symbols and populate the database: You can load Bio2BEL HGNC by running the following command in your terminal: python3 -m bio2bel_hgnc populate

Functionalities and Commands

Following, the main functionalities and commands to work with this package:

• Populate local database with WikiPathways info python3 -m bio2bel_wikipathways populate

• 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