Metadata-Version: 1.1
Name: bio2bel_reactome
Version: 0.2.2
Summary: A wrapper around Reactome RESTful API
Home-page: https://github.com/bio2bel/reactome
Author: Daniel Domingo-Fernández and Charles Tapley Hoyt
Author-email: daniel.domingo.fernandez@scai.fraunhofer.de
License: MIT License
Description-Content-Type: UNKNOWN
Description: Bio2BEL Reactome |build| |coverage| |documentation| |zenodo|
        ============================================================
        This package allows the enrichment of BEL networks with Reactome information by wrapping its RESTful API.
        Furthermore, it is integrated in the `ComPath environment <https://github.com/ComPath>`_ for pathway database
        comparison.
        
        Installation
        ------------
        This code can be installed with :code:`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:
        
        - :code:`python3 -m bio2bel_hgnc populate`
        - :code:`python3 -m bio2bel_chebi populate`
        
        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
        
            $ python3 -m pip install bio2bel_reactome
        
        or from the latest code on `GitHub <https://github.com/bio2bel/reactome>`_ with:
        
        .. code-block:: sh
        
            $ python3 -m pip install git+https://github.com/bio2bel/reactome.git@master
        
        Setup
        -----
        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:
        
        - `Bio2BEL CHEBI <https://github.com/bio2bel/chebi>`_
        - `Bio2BEL HGNC <https://github.com/bio2bel/hgnc>`_
        
        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:`python3 -m bio2bel_reactome web` (http://localhost:5000/admin/)
        - Export gene sets for programmatic use :code:`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.
        
        .. |build| image:: https://travis-ci.org/bio2bel/reactome.svg?branch=master
            :target: https://travis-ci.org/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
        
        .. |documentation| image:: http://readthedocs.org/projects/bio2bel-interpro/badge/?version=latest
            :target: http://bio2bel.readthedocs.io/projects/reactome/en/latest/?badge=latest
            :alt: Documentation Status
        
        .. |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
        
Keywords: Biological Expression Language,BEL,Reactome,Systems Biology,Networks Biology
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
