README.rst

Bio2BEL Reactome

This package handles the nomenclature and membership of chemicals/proteins in Reactome pathways. It is integrated with 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 Reactome mechanistic relationships to BEL. That functionality is implemented in the PathMe project.

Installation

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

$ pip install bio2bel_reactome

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

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

Setup

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

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 bio2bel_reactome web (http://localhost:5000/admin/)
• Export gene sets for programmatic use 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.