Metadata-Version: 2.1
Name: compath_resources
Version: 0.1.1
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.
        
        💾 Data
        -------
        A total of 6 mapping files are stored in this package, one for each pairwise comparison [*]_.
        These data are available under the CC0 1.0 Universal License.
        
        - `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.
        
        Update: March 2020
        ~~~~~~~~~~~~~~~~~~
        Mappings between `PathBank <https://pathbank.org/>`_ and the above-mentioned databases are now available in ComPath.
        
        📊 Summary
        ----------
        A summary is automatically generated nightly with GitHub Actions and deployed to
        https://compath.github.io/compath-resources/.
        
        🙏 Contributing
        ---------------
        While it's possible to improve the files in this repository, they have been integrated into a more
        general effort for identifying mappings between biological entities,
        `Biomappings <https://github.com/biomappings/biomappings>`_. Please direct contributions to that repository
        following its `curation guidelines <https://github.com/biomappings/biomappings#-contributing>`_.
        
        Curation Guidelines
        ~~~~~~~~~~~~~~~~~~~
        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
        
        ⬇️ Installation
        ---------------
        Download the latest stable code from `PyPI <https://pypi.python.org/pypi/compath_resources>`_ with:
        
        .. code-block:: python
        
           pip install compath_resources
        
        Download the most recent code from `GitHub <https://github.com/ComPath/compath-resources>`_ with:
        
        .. code-block:: python
        
           pip install git+https://github.com/ComPath/compath-resources.git
        
        💪 Usage
        --------
        .. code-block:: python
        
           import compath_resources
        
           # get all mappings as a pandas dataframe
           df = compath_resources.get_df()
        
           # get all mappings as a PyBEL BEL graph
           bel_graph = compath_resources.get_bel()
        
           # get all mappings as an RDFLib graph.
           rdf_graph = compath_resources.get_rdf()
        
        ⚖️ License
        ----------
        Code is licensed under the MIT License. Curated mappings are licensed under the CC-0 License.
        
        Acknowledgements
        ----------------
        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>`_
        
        .. |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
