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        "author": "Gijs Kant",
        "author_email": "gijs@thehyve.nl",
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            "Development Status :: 2 - Pre-Alpha",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "################################################################################\nExample ontology to TranSMART loader\n################################################################################\n\n|Build status| |codecov| |pypi| |downloads|\n\n.. |Build status| image:: https://travis-ci.org/thehyve/python_ontology2transmart.svg?branch=master\n   :alt: Build status\n   :target: https://travis-ci.org/thehyve/python_ontology2transmart/branches\n.. |codecov| image:: https://codecov.io/gh/thehyve/python_ontology2transmart/branch/master/graph/badge.svg\n   :alt: codecov\n   :target: https://codecov.io/gh/thehyve/python_ontology2transmart\n.. |pypi| image:: https://img.shields.io/pypi/v/ontology2transmart.svg\n   :alt: PyPI\n   :target: https://pypi.org/project/ontology2transmart/\n.. |downloads| image:: https://img.shields.io/pypi/dm/ontology2transmart.svg\n   :alt: PyPI - Downloads\n   :target: https://pypi.org/project/ontology2transmart/\n\nThis package contains a mapper that reads ontologies from DIMDI_ (Deutsche Institut f\u00fcr Medizinische Dokumentation und Information)\nand translates them to the data model of the TranSMART_ platform,\nan open source data sharing and analytics platform for translational biomedical research.\n\nIt also provides a utility that applies the mapper and writes the translated data to tab-separated files\nthat can be loaded into a TranSMART database using the transmart-copy_ tool.\n\n\u26a0\ufe0f Note: this is a very preliminary version, still under development.\nIssues can be reported at https://github.com/thehyve/python_ontology2transmart/issues.\n\n.. _DIMDI: https://www.dimdi.de\n.. _TranSMART: https://github.com/thehyve/transmart_core\n.. _transmart-copy: https://github.com/thehyve/transmart-core/tree/dev/transmart-copy\n.. _transmart-loader: https://pypi.org/project/transmart-loader\n\n\nInstallation\n------------\n\nThe package requires Python 3.6.\n\nTo install ``ontology2transmart``, do:\n\n.. code-block:: bash\n\n  pip install ontology2transmart\n\nOr from source:\n\n.. code-block:: bash\n\n  git clone https://github.com/thehyve/python_ontology2transmart.git\n  cd python_ontology2transmart\n  pip install .\n\n\nRun tests (including coverage) with:\n\n.. code-block:: bash\n\n  python setup.py test\n\n\nUsage\n-----\n\nRead ontology from a collection of TSV files from `DIMDI`_ and write the output in transmart-copy\nformat to ``/path/to/output``. The output directory should be\nempty of not existing (then it will be created).\n\n.. code-block:: bash\n\n  ontology2transmart <system> <chapters> <groups> <codes> /path/to/output\n\nParameters:\n\n:``system``:           Unique identifier for the ontology\n:``chapters``:         Semicolon-separated file with chapters\n:``groups``:           Semicolon-separated file with groups\n:``codes``:            Semicolon-separated file with codes\n:``/path/to/output``:  Output directory\n\nExample: the ICD-10-GM (German modification of ICD-10) is available at icd10gm2019syst-meta.zip_.\n\n.. _icd10gm2019syst-meta.zip: https://www.dimdi.de/dynamic/.downloads/klassifikationen/icd-10-gm/version2019/icd10gm2019syst-meta.zip\n\n.. code-block:: bash\n\n  # Unzip and navigate to the classification directory\n  mkdir icd10gm2019\n  cd icd10gm2019\n  unzip ../icd10gm2019syst-meta.zip\n  cd Klassifikationsdateien\n  # create an output directory\n  mkdir output\n  # apply the mapping\n  ontology2transmart http://dimdi.de/icd10gm2019 icd10gm2019syst_kapitel.txt icd10gm2019syst_gruppen.txt icd10gm2019syst_kodes.txt output\n\nThis generates the directories ``i2b2metadata`` and ``i2b2demodata`` in the ``output`` directory.\nThe generated data can be loaded using transmart-copy_:\n\n.. code-block:: console\n\n  # Download transmart-copy:\n  curl -f -L https://repo.thehyve.nl/service/local/repositories/releases/content/org/transmartproject/transmart-copy/17.1-HYVE-5.9-RC3/transmart-copy-17.1-HYVE-5.9-RC3.jar -o transmart-copy.jar\n  # Load data\n  PGUSER=tm_cz PGPASSWORD=tm_cz java -jar transmart-copy.jar -d output\n\n\nLicense\n-------\n\nCopyright (c) 2019 The Hyve B.V.\n\nThe ontology to TranSMART loader is licensed under the MIT License. See the file `<LICENSE>`_.\n\n\n\n\n",
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