{
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        "author": "Yifan Peng",
        "author_email": "yifan.peng@nih.gov",
        "bugtrack_url": null,
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            "Operating System :: MacOS",
            "Operating System :: Microsoft :: Windows",
            "Operating System :: POSIX",
            "Operating System :: POSIX :: Linux",
            "Programming Language :: Python",
            "Topic :: Software Development",
            "Topic :: Software Development :: Libraries :: Application Frameworks",
            "Topic :: Text Processing :: Markup :: XML"
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        "description": "`bioc` - BioC data structures and encoder/decoder for Python\n=============================================================\n\n.. image:: https://img.shields.io/travis/yfpeng/bioc.svg\n   :alt: Build status\n   :target: https://travis-ci.org/yfpeng/bioc\n\n.. image:: https://github.com/yfpeng/bioc/workflows/bioc/badge.svg\n   :alt: Build status\n   :target: https://github.com/yfpeng/bioc/\n\n.. image:: https://img.shields.io/pypi/v/bioc.svg\n   :target: https://pypi.python.org/pypi/bioc\n   :alt: Latest version on PyPI\n\n.. image:: https://img.shields.io/pypi/dm/bioc.svg\n   :alt: Downloads\n   :target: https://pypi.python.org/pypi/bioc\n   \n.. image:: https://coveralls.io/repos/github/yfpeng/bioc/badge.svg?branch=master\n   :alt: Coverage\n   :target: https://pypi.python.org/pypi/bioc\n   \n.. image:: https://requires.io/github/yfpeng/bioc/requirements.svg?branch=master\n   :target: https://requires.io/github/yfpeng/bioc/requirements/?branch=master\n   :alt: Requirements Status\n\n.. image:: https://img.shields.io/pypi/l/bioc.svg\n   :alt: License\n   :target: https://opensource.org/licenses/BSD-3-Clause\n\n\n`BioC XML / JSON format <http://bioc.sourceforge.net/>`_ can be used to share\ntext documents and annotations.\n\n``bioc`` exposes an API familiar to users of the standard library\n``marshal`` and ``pickle`` modules.\n\nDevelopment of ``bioc`` happens on GitHub:\nhttps://github.com/yfpeng/bioc\n\nGetting started\n---------------\n\nInstalling ``bioc``\n\n.. code:: bash\n\n    $ pip install bioc\n\nXML\n~~~\n\nEncoding the BioC collection object ``collection``:\n\n.. code:: python\n\n    import bioc\n    # Serialize ``collection`` to a BioC formatted ``str``.\n    bioc.dumps(collection)\n\n    # Serialize ``collection`` as a BioC formatted stream to ``fp``.\n    with open(filename, 'w') as fp\n        bioc.dump(collection, fp)\n\nCompact encoding:\n\n.. code:: python\n\n    import bioc\n    bioc.dumps(collection, pretty_print=False)\n\nIncremental BioC serialisation:\n\n.. code:: python\n\n    import bioc\n    with bioc.BioCXMLDocumentWriter(filename) as writer:\n        writer.write_collection_info(collection)\n        for document in collection.documents:\n            writer.write_document(document)\n\nDecoding the BioC XML file:\n\n.. code:: python\n\n    import bioc\n    # Deserialize ``s`` to a BioC collection object.\n    collection = bioc.loads(s)\n\n    # Deserialize ``fp`` to a BioC collection object.\n    with open(filename, 'r') as fp:\n        collection = bioc.load(fp)\n\nIncrementally decoding the BioC XML file:\n\n.. code:: python\n\n    import bioc\n    with bioc.BioCXMLDocumentReader(filename) as reader:\n        collection_info = reader.get_collection_info()\n        for document in reader:\n            # process document\n            ...\n\n``get_collection_info`` can be called after the construction of the ``BioCXMLDocumentReader`` anytime.\n\nTogether with Python coroutines, this can be used to generate BioC XML in an asynchronous, non-blocking fashion.\n\n.. code:: python\n\n    import bioc\n    with bioc.BioCXMLDocumentReader(source) as reader, \\\n         bioc.BioCXMLDocumentWriter(dest) as writer:\n        collection_info = reader.get_collection_info()\n        writer.write_collection_info(collection_info)\n        for document in reader:\n            # modify the document\n            ...\n            writer.write_document(document)\n\nJson\n~~~~\n\nEncoding the BioC collection object ``collection``:\n\n.. code:: python\n\n    import biocjson\n    # Serialize ``collection`` to a BioC Json formatted ``str``.\n    biocjson.dumps(collection, indent=2)\n\n    # Serialize ``collection`` as a BioC Json formatted stream to ``fp``.\n    with open(filename, 'w') as fp\n        biocjson.dump(collection, fp, indent=2)\n\nCompact encoding:\n\n.. code:: python\n\n    import biocjson\n    biocjson.dumps(collection)\n\nDecoding the BioC Json file:\n\n.. code:: python\n\n    import biocjson\n    # Deserialize ``s`` to a BioC collection object.\n    collection = biocjson.loads(s)\n\n    # Deserialize ``fp`` to a BioC collection object.\n    with open(filename, 'r') as fp:\n        collection = biocjson.load(fp)\n\nJson Lines\n~~~~~~~~~~\n\nIncrementally encoding the BioC structure:\n\n.. code:: python\n\n    from bioc.biocjson import BioCJsonIterWriter\n    with BioCJsonIterWriter(filename, level=bioc.PASSAGE) as writer:\n        for doc in collection.documents:\n             for passage in doc.passages:\n                 writer.write(passage)\n\nor\n\n.. code:: python\n\n    from bioc.biocjson import toJSON\n    import jsonlines\n    with jsonlines.open(filename, 'w') as writer:\n        for doc in collection.documents:\n             for passage in doc.passages:\n                 writer.write(toJSON(passage))\n\nIncrementally decoding the BioC Json lines file:\n\n.. code:: python\n\n    from bioc.biocjson import BioCJsonIterReader\n    with BioCJsonIterReader(filename, level=bioc.PASSAGE) as reader:\n        for passage in reader:\n            # process passage\n            ...\n\nor\n\n.. code:: python\n\n    from bioc.biocjson import fromJSON\n    import jsonlines\n    with jsonlines.open(filename) as reader:\n        for obj in reader:\n            passage = fromJSON(obj, level=bioc.PASSAGE)\n            ...\n\nDevelopers\n----------\n\n-  Yifan Peng (yifan.peng@nih.gov)\n\nAcknowledgment\n--------------\n\n-  Hernani Marques (https://github.com/2mh/PyBioC)\n\nWebpage\n-------\n\nThe official BioC webpage is available with all up-to-date instructions,\ncode, and corpora in the BioC format, and other research on, based on\nand related to BioC.\n\n-  http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/\n-  http://bioc.sourceforge.net/\n\n\nReference\n---------\n\nIf you use bioc in your research, please cite the following paper:\n\n-  Peng,Y., Tudor,C., Torii,M., Wu,C.H., Vijay-Shanker,K. (2014) iSimp\n   in BioC standard format: Enhancing the interoperability of a sentence\n   simplification system. Database: The Journal of Biological Databases\n   and Curation.",
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