bio2bel-reactome 0.0.4

A wrapper around Reactome RESTful API

This package allows the enrichment of BEL networks with Reactome 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/reactome.git

Note that the two following resources should be installed and loaded in order to fully populate the tables of the database:

• Bio2BEL CHEBI

• Bio2BEL HGNC

These two resources will be installed together with this package and can be quickly loaded by running the following commands in your terminal:

• python3 -m bio2bel_hgnc populate

• python3 -m bio2bel_chebi populate

Functionalities and Commands

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

• Populate local database with Reactome info python3 -m bio2bel_reactome populate

• Run an admin site for simple querying and exploration python3 -m bio2bel_reactome web (http://localhost:5000/admin/)

• Export gene sets for programmatic use python3 -m bio2bel_reactome export

Citation

• Fabregat, Antonio et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research 44.Database issue (2016): D481–D487. PMC. Web. 6 Oct. 2017.

• Croft, David et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research 42.Database issue (2014): D472–D477. PMC. Web. 6 Oct. 2017.