{
    "info": {
        "author": "Christian Ebeling",
        "author_email": "christian.ebeling@scai.fraunhofer.de",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Database",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "PyCTD |stable_build|\n====================\n\n|stable_documentation| |pypi_license|\n\n`PyCTD <http://pyctd.readthedocs.io>`_ is a Python package\nto access and query chemical\u2013gene/protein interactions, chemical\u2013disease and gene\u2013disease\nrelationships by data provided by the `Comparative Toxicogenomics Database <http://ctdbase.org>`_ .\nData are installed in a (local or remte) RDBMS enabling bioinformatic algorithms very fast response times\nto sophisticated queries and high flexibility by using SQLAlchemy database layer.\nPyCTD is developed by the\n`Department of Bioinformatics <https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics.html>`_\nat the Fraunhofer Institute for Algorithms and Scientific Computing\n`SCAI <https://www.scai.fraunhofer.de/en.html>`_\nFor more in for information about CTD go to\n`this section in the documentation <http://pyctd.readthedocs.io/en/latest/ctd.html>`_.\n\n|er_model|\n\nThis development is supported by following `IMI <https://www.imi.europa.eu/>`_ projects:\n\n- `AETIONOMY <http://www.aetionomy.eu/>`_ and\n- `PHAGO <http://www.phago.eu/>`_.\n\n|imi_logo| |aetionomy_logo| |phago_logo| |scai_logo|\n\nSupported Databases\n-------------------\n\n`PyCTD` uses `SQLAlchemy <http://sqlalchemy.readthedocs.io>`_ to cover a wide spectrum of RDMSs\n(Relational database management system). For best performance MySQL or MariaDB is recommended. But if you have no\npossibility to install software on your system SQLite - which needs no further\ninstallation - also works. Following RDMSs are supported (by SQLAlchemy):\n\n1. Firebird\n2. Microsoft SQL Server\n3. MySQL / `MariaDB <https://mariadb.org/>`_\n4. Oracle\n5. PostgreSQL\n6. SQLite\n7. Sybase\n\nGetting Started\n---------------\nThis is a quick start tutorial for impatient.\n\nInstallation |pypi_version| |python_versions|\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nPyCTD can be installed with `pip <https://pip.pypa.io/en/stable/>`_.\n\n.. code-block:: bash\n\n    pip install pyctd\n\nIf you fail because you have no rights to install use superuser (sudo on Linux before the commend) or ...\n\n.. code-block:: bash\n\n    pip install --user pyctd\n\nIf you want to make sure you are installing this under python3 use ...\n\n.. code-block:: bash\n\n    python3 -m pip install pyctd\n\nSQLite\n~~~~~~\n.. note:: If you want to use SQLite as your database system, because you ...\n\n    - have no possibility to use RDMSs like MySQL/MariaDB\n    - just test pyctd, but don't want to spend time in setting up a database\n\n    skip the next *MySQL/MariaDB setup* section. But in general we recommend MySQL or MariaDB as your RDBMS.\n\nIf you don't know what all that means skip the section *MySQL/MariaDB setup*.\n\nDon't worry! You can always later change the configuration. For more information about\nchanging database system later go to the subtitle *Changing database configuration*\n`Changing database configuration <http://pyctd.readthedocs.io/en/latest/installation.html>`_\nin the documentation on readthedocs.\n\nMySQL/MariaDB Setup\n~~~~~~~~~~~~~~~~~~~\nLog in MySQL as root user and create a new database, create a user, assign the rights and flush privileges.\n\n.. code-block:: mysql\n\n    CREATE DATABASE pyctd CHARACTER SET utf8 COLLATE utf8_general_ci;\n    GRANT ALL PRIVILEGES ON pyctd.* TO 'pyctd_user'@'%' IDENTIFIED BY 'pyctd_passwd';\n    FLUSH PRIVILEGES;\n\nStart a python shell and set the MySQL configuration. If you have not changed anything in the SQL statements ...\n\n.. code-block:: python\n\n    import pyctd\n    pyctd.set_mysql_connection()\n\nIf you have used you own settings, please adapt the following command to you requirements.\n\n.. code-block:: python\n\n    import pyctd\n    pyctd.set_mysql_connection(host='localhost', user='pyctd_user', passwd='pyctd_passwd', db='pyctd')\n\nUpdating\n~~~~~~~~\nThe updating process will download the files provided by the CTD team on the\n`download page <http://ctdbase.org/downloads/>`_\n\n.. warning:: Please note that download files needs 1,5Gb of disk space and the update takes ~2h (depending on your system)\n\n.. code-block:: python\n\n    import pyctd\n    pyctd.update()\n\nExample Query\n~~~~~~~~~~~~~\n.. code-block:: python\n\n    >>> query = pyctd.query()\n    >>> results = query.get_chem_gene_interaction_actions(gene_name='APP', interaction_action='meman%', limit=1)\n    >>> first_result = r\n    >>> r.chemical\n    Memantine\n    >>> r.pubmed_ids\n    [21290839]\n    >>> r.chemical.drugbank_ids\n    [DB014043]\n\n\nMore Information\n----------------\nSee the `installation documentation <http://pyctd.readthedocs.io/en/latest/installation.html>`_ for more advanced\ninstructions. Also, check the change log at :code:`CHANGELOG.rst`.\n\nCTD Tools and License (use of data)\n-----------------------------------\nCTD provides also many online `query interfaces <http://ctdbase.org/search/>`_ and\n`tools to analyse data <http://ctdbase.org/tools/>`_ on their website.\n\nPlease be aware of the `CTD license <http://ctdbase.org/about/legal.jsp>`_ which allows the use of data only for\nresearch and educational purposes. Medical treatment decisions should not be made based on the information in CTD.\n\nAny reproduction or use for commercial purpose is prohibited without the prior express written permission of the\nMDI Biological Laboratory and NC State University.\n\n\nLinks\n-----\nComparative Toxicogenomics Database (CTD)\n\n- `CTD website <http://ctdbase.org/>`_\n- `All CTD publications <http://ctdbase.org/about/publications/>`_\n- `CTD download page <http://ctdbase.org/downloads/>`_\n\nPyCTD\n\n- Documented on `Read the Docs <http://pyctd.readthedocs.io/>`_\n- Versioned on `GitHub <https://github.com/cebel/pyctd>`_\n- Tested on `Travis CI <https://travis-ci.org/cebel/pyctd>`_\n- Distributed by `PyPI <https://pypi.python.org/pypi/pyctd>`_\n- Chat on `Gitter <https://gitter.im/pyctd/Lobby>`_\n\n.. |stable_build| image:: https://travis-ci.org/cebel/pyctd.svg?branch=master\n    :target: https://travis-ci.org/cebel/pyctd\n    :alt: Stable Build Status\n\n.. |stable_documentation| image:: https://readthedocs.org/projects/pyctd/badge/?version=latest\n    :target: http://pyctd.readthedocs.io/en/latest/\n    :alt: Development Documentation Status\n\n.. |pypi_license| image:: https://img.shields.io/pypi/l/PyCTD.svg\n    :alt: Apache 2.0 License\n\n.. |python_versions| image:: https://img.shields.io/pypi/pyversions/PyCTD.svg\n    :alt: Stable Supported Python Versions\n\n.. |pypi_version| image:: https://img.shields.io/pypi/v/PyCTD.svg\n    :alt: Current version on PyPI\n\n.. |phago_logo| image:: https://owncloud.scai.fraunhofer.de/index.php/apps/files_sharing/ajax/publicpreview.php?x=1920&y=562&a=true&file=phago-logo.jpg&t=7llp11KwSiuXYOh&scalingup=0\n    :target: https://www.imi.europa.eu/content/phago\n    :alt: PHAGO project logo\n\n.. |aetionomy_logo| image:: https://owncloud.scai.fraunhofer.de/index.php/apps/files_sharing/ajax/publicpreview.php?x=1920&y=562&a=true&file=aetionomy-logo.png&t=5ClUGTZRAYkeb7m&scalingup=0\n    :target: http://www.aetionomy.eu/en/vision.html\n    :alt: AETIONOMY project logo\n\n.. |imi_logo| image:: https://owncloud.scai.fraunhofer.de/index.php/apps/files_sharing/ajax/publicpreview.php?x=1920&y=562&a=true&file=imi-logo.png&t=Uvw79bTxGyd07oo&scalingup=0\n    :target: https://www.imi.europa.eu/\n    :alt: IMI project logo\n\n.. |scai_logo| image:: https://owncloud.scai.fraunhofer.de/index.php/apps/files_sharing/ajax/publicpreview.php?x=1920&y=562&a=true&file=scai-logo.png&t=fyJo2GzFDLNypho&scalingup=0\n    :target: https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics.html\n    :alt: SCAI project logo\n\n.. |er_model| image:: https://owncloud.scai.fraunhofer.de/index.php/apps/files_sharing/ajax/publicpreview.php?x=1920&y=562&a=true&file=pyctd_er_model.png&t=QUm8KPPnNGoH8wp&scalingup=0\n    :target: http://pyctd.readthedocs.io/en/latest/\n    :alt: Entity relationship model",
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