bio2bel-reactome 0.2.0

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

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

Installation

bio2bel_reactome can be installed easily from PyPI with the following code in your favorite terminal:

$ python3 -m pip install bio2bel_reactome

or from the latest code on GitHub with:

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

Setup

Reactome 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 CHEBI

• Bio2BEL HGNC

Python REPL

>>> import bio2bel_reactome
>>> reactome_manager = bio2bel_reactome.Manager()
>>> reactome_manager.populate()

Command Line Utility

bio2bel_reactome populate

Other Command Line Utilities

• 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.