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.
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
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
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:
>>> import bio2bel_reactome >>> reactome_manager = bio2bel_reactome.Manager() >>> reactome_manager.populate()
Command Line Utility
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
- 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.