Metadata-Version: 2.1
Name: bio2bel-wikipathways
Version: 0.0.6
Summary: A package for converting Wikipathways to BEL
Home-page: https://github.com/bio2bel/wikipathways
Author: Daniel Domingo-Fernández and Charles Tapley Hoyt
Author-email: daniel.domingo.fernandez@scai.fraunhofer.de
Maintainer: Daniel Domingo-Fernández and Charles Tapley Hoyt
Maintainer-email: daniel.domingo.fernandez@scai.fraunhofer.de
License: MIT License
Description: Bio2BEL WikiPathways |build| |coverage| |docs|
        ==============================================
        This package allows the enrichment of BEL networks with WikiPathways 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/wikipathways.git`
        
        Note that the `Bio2BEL HGNC <https://github.com/bio2bel/hgnc>`_ should be installed and loaded in order to map ENTREZ identifiers to HGNC Symbols and populate the database:
        You can load Bio2BEL HGNC by running the following command in your terminal: :code:`python3 -m bio2bel_hgnc populate`
        
        Functionalities and Commands
        ----------------------------
        Following, the main functionalities and commands to work with this package:
        
        - Populate local database with WikiPathways info :code:`python3 -m bio2bel_wikipathways populate`
        - Run an admin site for simple querying and exploration :code:`python3 -m bio2bel_wikipathways web` (http://localhost:5000/admin/)
        - Export gene sets for programmatic use :code:`python3 -m bio2bel_wikipathways export`
        
        Citation
        --------
        
        - Slenter, D.N., et al WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research Nucleic Acids Research, (2017)doi.org/10.1093/nar/gkx1064
        
        - Kutmon, M., et al. WikiPathways: capturing the full diversity of pathway knowledge Nucl. Acids Res., 44, D488-D494 (2016) doi:10.1093/nar/gkv1024
        
        - Kelder, T., et al. WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 2012 Jan;40(Database issue):D1301-7
        
        
        .. |build| image:: https://travis-ci.org/bio2bel/wikipathways.svg?branch=master
            :target: https://travis-ci.org/bio2bel/wikipathways
            :alt: Build Status
        
        .. |coverage| image:: https://codecov.io/gh/bio2bel/wikipathways/coverage.svg?branch=master
            :target: https://codecov.io/gh/bio2bel/wikipathways?branch=master
            :alt: Coverage Status
        
        .. |docs| image:: http://readthedocs.org/projects/bio2bel-wikipathways/badge/?version=latest
            :target: http://bio2bel.readthedocs.io/projects/wikipathways/en/latest/?badge=latest
            :alt: Documentation Status
        
Platform: UNKNOWN
Provides-Extra: web
