Metadata-Version: 2.1
Name: bio2bel-kegg
Version: 0.3.0
Summary: A package for converting KEGG gene sets into BEL
Home-page: https://github.com/bio2bel/kegg
Author: Daniel Domingo-Fernández and Charles Tapley Hoyt
Author-email: daniel.domingo.fernandez@scai.fraunhofer.de
Maintainer: Charles Tapley Hoyt
Maintainer-email: cthoyt@gmail.com
License: MIT
Download-URL: https://github.com/bio2bel/kegg/releases
Project-URL: Bug Tracker, https://github.com/bio2bel/kegg/issues
Project-URL: Source Code, https://github.com/bio2bel/kegg
Description: Bio2BEL KEGG |build| |coverage| |documentation| |zenodo|
        ========================================================
        This package allows the enrichment of BEL networks with KEGG information by wrapping its RESTful API.
        Furthermore, it is integrated in 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 KEGG 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_kegg`` can be installed easily from `PyPI <https://pypi.python.org/pypi/bio2bel_kegg>`_ with the
        following code in your favorite terminal:
        
        .. code-block:: sh
        
            $ pip install bio2bel_kegg
        
        or from the latest code on `GitHub <https://github.com/bio2bel/kegg>`_ in development mode with:
        
        .. code-block:: sh
        
            $ git clone https://github.com/bio2bel/kegg.git
            $ cd kegg
            $ pip install -e .
        
        Setup
        -----
        KEGG can be downloaded and populated from either the Python REPL or the automatically installed command line utility.
        
        Python REPL
        ~~~~~~~~~~~
        .. code-block:: python
        
            >>> import bio2bel_kegg
            >>> kegg_manager = bio2bel_kegg.Manager()
            >>> kegg_manager.populate()
        
        Command Line Utility
        ~~~~~~~~~~~~~~~~~~~~
        .. code-block:: bash
        
            bio2bel_kegg populate
        
        Other Command Line Utilities
        ----------------------------
        - Run an admin site for simple querying and exploration :code:`python3 -m bio2bel_kegg web`
          (http://localhost:5000/admin/)
        - Export gene sets for programmatic use :code:`python3 -m bio2bel_kegg export`
        
        Citation
        --------
        - Kanehisa, Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K.; KEGG: new perspectives on genomes,
          pathways, diseases and drugs. Nucleic Acids Res. 45, D353-D361 (2017).
        - Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; KEGG as a reference resource
          for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016).
        - Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).
        
        .. |build| image:: https://travis-ci.org/bio2bel/kegg.svg?branch=master
            :target: https://travis-ci.org/bio2bel/kegg
            :alt: Build Status
        
        .. |coverage| image:: https://codecov.io/gh/bio2bel/kegg/coverage.svg?branch=master
            :target: https://codecov.io/gh/bio2bel/kegg?branch=master
            :alt: Coverage Status
        
        .. |documentation| image:: http://readthedocs.org/projects/bio2bel-interpro/badge/?version=latest
            :target: http://bio2bel.readthedocs.io/projects/kegg/en/latest/?badge=latest
            :alt: Documentation Status
        
        .. |climate| image:: https://codeclimate.com/github/bio2bel/kegg/badges/gpa.svg
            :target: https://codeclimate.com/github/bio2bel/kegg
            :alt: Code Climate
        
        .. |python_versions| image:: https://img.shields.io/pypi/pyversions/bio2bel_kegg.svg
            :alt: Stable Supported Python Versions
        
        .. |pypi_version| image:: https://img.shields.io/pypi/v/bio2bel_kegg.svg
            :alt: Current version on PyPI
        
        .. |pypi_license| image:: https://img.shields.io/pypi/l/bio2bel_kegg.svg
            :alt: MIT License
        
        .. |zenodo| image:: https://zenodo.org/badge/105248163.svg
            :target: https://zenodo.org/badge/latestdoi/105248163
        
Keywords: Biological Expression Language,BEL,Systems Biology,KEGG
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 :: 3.7
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7
Provides-Extra: docs
