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.
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 .
Reactome can be downloaded and populated from either the Python REPL or the automatically installed command line utility.
>>> import bio2bel_reactome
>>> reactome_manager = bio2bel_reactome.Manager()
>>> reactome_manager.populate()
bio2bel_reactome populate
- Run an admin site for simple querying and exploration
bio2bel_reactome web
(https://localhost:5000/admin/) - Export gene sets for programmatic use
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.