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    "info": {
        "author": "Daniel Domingo-Fern\u00e1ndez",
        "author_email": "daniel.domingo.fernandez@scai.fraunhofer.de",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 1 - Planning",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: 3 :: Only"
        ],
        "description": "ComPath Resources |zenodo|\n==========================\nThis repository contains the different resources derived or generated using `ComPath <https://github.com/ComPath>`_.\nAmong these resources, there are `Jupyter notebooks <https://github.com/ComPath/resources/tree/master/notebooks>`_\noutlining possible analyses that can be made using ComPath plugins as well as the results of the curation effort\n`('mappings' folder) <https://github.com/ComPath/resources/tree/master/mappings>`_ where we generated pathway mappings\nbetween three of the major pathway databases (see below).\n\nCitation\n--------\nIf you use ComPath in your work, please cite [1]_:\n\n.. [1] Domingo-Fern\u00e1ndez, D., *et al.* (2019). `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.*, 5(1):3.\n\nInstallation |pypi_version| |python_versions| |pypi_license|\n------------------------------------------------------------\n\nEasiest\n~~~~~~~\nDownload the latest stable code from `PyPI <https://pypi.python.org/pypi/compath_resources>`_ with:\n\n.. code-block:: python\n\n   python3 -m pip install compath_resources\n\nGet the Latest\n~~~~~~~~~~~~~~~\nDownload the most recent code from `GitHub <https://github.com/ComPath/resources>`_ with:\n\n.. code-block:: python\n\n   python3 -m pip install git+https://github.com/ComPath/resources.git@master\n\nCuration (Pathway Mappings)\n~~~~~~~~~~~~~~~~~~~~~~~~~~~\nThe aim of this exercise was to generate mapping files across pathway databases in order to establish relationships\nbetween similar pathways in three of the major pathway databases:\n\n- `KEGG <http://www.kegg.jp/>`_\n- `Reactome <http://reactome.org/>`_\n- `WikiPathways <https://www.wikipathways.org/index.php/WikiPathways>`_\n\n*We recommend to download the mappings directly from the ComPath website since the pathways in WikiPathways are not\nstable and might have been changed. However, the mapping file distributed by the website contains stable identifiers\nfrom all resources.*\n\nMapping Between Pathway Databases\n---------------------------------\nA total of 3 mapping files are stored in this package, one for each pairwise comparison:\n\n- `KEGG - WikiPathways <https://github.com/ComPath/curation/blob/master/mappings/kegg_wikipathways.xlsx>`_\n- `KEGG - Reactome <https://github.com/ComPath/curation/blob/master/mappings/kegg_reactome.xlsx>`_\n- `WikiPathways - Reactome <https://github.com/ComPath/curation/blob/master/mappings/wikipathways_reactome.xlsx>`_\n\n*It is important to mention that even more mappings are stored in the database thanks to the ComPath inference system.\nFor example, when a KEGG to WikiPathways pathway is assigned as equivalent to a Reactome pathway, ComPath uses the\nReactome hierarchy to infer new hierarchical mappings and map the super/sub pathways of the Reactome pathway to this\ncorresponding equivalent pathway.*\n\nCuration Team\n-------------\nThe curation exercise was conducted under inter-curator agreement in a team formed by:\n\n- Carlos Bobis-\u00c1lvarez\n- Josep Mar\u00edn-Lla\u00f3\n- `Daniel Domingo-Fern\u00e1ndez <https://github.com/ddomingof>`_\n\nMapping Types\n-------------\nWe have distinguished between two types of relationships between pathways (mappings): \u201cequivalentTo\u201d and \u201cisPartOf\u201d.\n\n- equivalentTo. An undirected relationship denoting both pathways refer to the same biological process. The\n  requirements for this relationship are:\n\n  - Scope: both pathways represent the same biological pathway information.\n  - Similarity: both pathways must share at minimum of one overlapping gene.\n  - Context: both pathways should take place in the same context (e.g., cell line, physiology)\n\n- isPartOf. A directed relationship denoting the hierarchical relationship between the pathway 1 (child) and 2\n  (parent). The requirements are:\n\n  - Subset: The subject (pathway 1) is a subset of pathway 2 (e.g., Reactome pathway hierarchy). \n  - Similarity: same as above\n  - Context: same as above\n\n.. |python_versions| image:: https://img.shields.io/pypi/pyversions/compath_resources.svg\n    :alt: Stable Supported Python Versions\n.. |pypi_version| image:: https://img.shields.io/pypi/v/compath_resources.svg\n    :alt: Current version on PyPI\n.. |pypi_license| image:: https://img.shields.io/pypi/l/compath_resources.svg\n    :alt: MIT License\n.. |zenodo| image:: https://zenodo.org/badge/132792765.svg\n   :target: https://zenodo.org/badge/latestdoi/132792765\n\n\n",
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        "keywords": "KEGG,Reactome,WikiPathways,Biological Networks,Pathway Analysis,Networks Biology",
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        "maintainer": "Daniel Domingo-Fern\u00e1ndez",
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