Bio2BEL Reactome |build| |coverage| |documentation| |zenodo|

This package handles the nomenclature and membership of chemicals/proteins in Reactome pathways. It is integrated with the ComPath environment <https://github.com/ComPath>_ 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 <https://doi.org/10.1038/s41540-018-0078-8>_. 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 <https://github.com/pathwaymerger/pathme>_.

Installation |pypi_version| |python_versions| |pypi_license|

bio2bel_reactome can be installed easily from PyPI <https://pypi.python.org/pypi/bio2bel_reactome>_ with the following code in your favorite terminal:

.. code-block:: sh

$ pip install bio2bel_reactome

or from the latest code on GitHub <https://github.com/bio2bel/reactome>_ in development mode with:

.. code-block:: sh

$ 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

.. code-block:: python

    >>> import bio2bel_reactome
    >>> reactome_manager = bio2bel_reactome.Manager()
    >>> reactome_manager.populate()

Command Line Utility

.. code-block:: bash

bio2bel_reactome populate

Other Command Line Utilities

• Run an admin site for simple querying and exploration :code:bio2bel_reactome web (http://localhost:5000/admin/)
• Export gene sets for programmatic use :code: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.

.. |build| image:: https://travis-ci.com/bio2bel/reactome.svg?branch=master :target: https://travis-ci.com/bio2bel/reactome :alt: Build Status

.. |coverage| image:: https://codecov.io/gh/bio2bel/reactome/coverage.svg?branch=master :target: https://codecov.io/gh/bio2bel/reactome?branch=master :alt: Coverage Status

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.. |climate| image:: https://codeclimate.com/github/bio2bel/reactome/badges/gpa.svg :target: https://codeclimate.com/github/bio2bel/reactome :alt: Code Climate

.. |python_versions| image:: https://img.shields.io/pypi/pyversions/bio2bel_reactome.svg :alt: Stable Supported Python Versions

.. |pypi_version| image:: https://img.shields.io/pypi/v/bio2bel_reactome.svg :alt: Current version on PyPI

.. |pypi_license| image:: https://img.shields.io/pypi/l/bio2bel_reactome.svg :alt: MIT License

.. |zenodo| image:: https://zenodo.org/badge/103138323.svg :target: https://zenodo.org/badge/latestdoi/103138323