A wrapper around Reactome RESTful API
Project description
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:
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
Functionalities and Commands
Following, the main functionalities and commands to work with this package:
Populate local database with Reactome info
python3 -m bio2bel_reactome populateRun 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.
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