Metadata-Version: 2.1
Name: compath_resources
Version: 0.0.10
Summary: ComPath Resource Utilities
Home-page: https://github.com/compath/compath-resources
Author: Daniel Domingo-Fernández
Author-email: daniel.domingo.fernandez@scai.fraunhofer.de
Maintainer: Daniel Domingo-Fernández
Maintainer-email: daniel.domingo.fernandez@scai.fraunhofer.de
License: MIT
Download-URL: https://github.com/compath/compath-resources/releases
Project-URL: Bug Tracker, https://github.com/compath/compath-resources/issues
Description: ComPath Resources
        =================
        |tests| |pypi_version| |python_versions| |pypi_license| |zenodo|
        
        This repository contains the different resources derived or generated using `ComPath <https://github.com/ComPath>`_.
        Among these resources, there are `Jupyter notebooks <https://github.com/ComPath/compath-resources/tree/master/notebooks>`_
        outlining possible analyses that can be made using ComPath plugins as well as the results of the curation effort
        (see the `mappings <https://github.com/ComPath/compath-resources/tree/master/mappings>`_ folder) where pathway mappings between
        three of the major pathway databases (see below) are stored. As of March 2020, `PathBank <https://pathbank.org/>`_
        mappings are now available in ComPath.
        
        Citation
        --------
        If you use ComPath in your work, please consider citing:
        
        .. [1] Domingo-Fernández, 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 Syst Biol Appl.*, 4(1):43.
        
        Installation
        ------------
        Easiest
        ~~~~~~~
        Download the latest stable code from `PyPI <https://pypi.python.org/pypi/compath_resources>`_ with:
        
        .. code-block:: python
        
           python3 -m pip install compath_resources
        
        Get the Latest
        ~~~~~~~~~~~~~~~
        Download the most recent code from `GitHub <https://github.com/ComPath/compath-resources>`_ with:
        
        .. code-block:: python
        
           python3 -m pip install git+https://github.com/ComPath/compath-resources.git@master
            
        Curation (Pathway Mappings)
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~
        The aim of this exercise was to generate mapping files across pathway databases in order to establish relationships
        between similar pathways in three of the major pathway databases:
        
        - `KEGG <http://www.kegg.jp/>`_
        - `Reactome <http://reactome.org/>`_
        - `WikiPathways <https://www.wikipathways.org/index.php/WikiPathways>`_
        
        *We recommend to download the mappings directly from the ComPath website since the pathways in WikiPathways are not
        stable and might have been changed. However, the mapping file distributed by the website contains stable identifiers
        from all resources.*
        
        Update: March 2020
        ~~~~~~~~~~~~~~~~~~
        Mappings between `PathBank <https://pathbank.org/>`_ and the above-mentioned databases are now available in ComPath.
        
        Mapping Between Pathway Databases
        ---------------------------------
        A total of 6 mapping files are stored in this package, one for each pairwise comparison [*]_:
        
        - `KEGG - WikiPathways <https://github.com/ComPath/compath-resources/blob/master/mappings/kegg_wikipathways.csv>`_
        - `KEGG - Reactome <https://github.com/ComPath/compath-resources/blob/master/mappings/kegg_reactome.csv>`_
        - `WikiPathways - Reactome <https://github.com/ComPath/compath-resources/blob/master/mappings/wikipathways_reactome.csv>`_
        - `PathBank - KEGG <https://github.com/ComPath/compath-resources/blob/master/mappings/pathbank_kegg.csv>`_
        - `PathBank - Reactome <https://github.com/ComPath/compath-resources/blob/master/mappings/pathbank_reactome.csv>`_
        - `PathBank - WikiPathways <https://github.com/ComPath/compath-resources/blob/master/mappings/pathbank_wikipathways.csv>`_
        
        .. [*] Pairwise mappings between KEGG, Reactome and WikiPathways were last updated in March of 2019. PathBank mappings
            were last updated in March of 2020.
        
        Curation Team
        -------------
        The curation exercise was conducted under inter-curator agreement in a team formed by:
        
        - Carlos Bobis-Álvarez
        - `Josep Marín-Llaó <https://github.com/jmarinllao>`_
        - `Daniel Domingo-Fernández <https://github.com/ddomingof>`_
        - `Yojana Gadiya <https://github.com/YojanaGadiya>`_
        
        Mapping Types
        -------------
        We have distinguished between two types of relationships between pathways (mappings): “equivalentTo” and “isPartOf”.
        
        - equivalentTo. An undirected relationship denoting both pathways refer to the same biological process. The
          requirements for this relationship are:
        
          - Scope: both pathways represent the same biological pathway information.
          - Similarity: both pathways must share at minimum of one overlapping gene.
          - Context: both pathways should take place in the same context (e.g., cell line, physiology)
        
        - isPartOf. A directed relationship denoting the hierarchical relationship between the pathway 1 (child) and 2
          (parent). The requirements are:
        
          - Subset: The subject (pathway 1) is a subset of pathway 2 (e.g., Reactome pathway hierarchy). 
          - Similarity: same as above
          - Context: same as above
          
        .. |python_versions| image:: https://img.shields.io/pypi/pyversions/compath_resources.svg
            :alt: Stable Supported Python Versions
        .. |pypi_version| image:: https://img.shields.io/pypi/v/compath_resources.svg
            :target: https://pypi.python.org/pypi/compath_resources
            :alt: Current version on PyPI
        .. |pypi_license| image:: https://img.shields.io/pypi/l/compath_resources.svg
            :alt: MIT License
        .. |zenodo| image:: https://zenodo.org/badge/132792765.svg
           :target: https://zenodo.org/badge/latestdoi/132792765
        .. |tests| image:: https://github.com/ComPath/compath-resources/workflows/Tests/badge.svg
           :target: https://github.com/ComPath/compath-resources/actions?query=workflow%3ATests
        
Keywords: KEGG,Reactome,WikiPathways,PathBank,Biological Networks,Pathway Analysis,Networks Biology
Platform: UNKNOWN
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.7
Provides-Extra: docs
Provides-Extra: rdf
