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 populatepython3 -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_reactomeor from the latest code on GitHub with:
$ python3 -m pip install git+https://github.com/bio2bel/reactome.git@masterReactome 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()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
- 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.