BioC-JSON is a tool that converts between BioC XML files and BioC JSON files. BioC is a simple data structure to share text data and annotations. More information is available at http://bioc.sourceforge.net.
When it was first implemented, XML was used for serialization. Now a lot of data exchange occurs in JSON. The BioC data structures have now been implemented in JSON. The JSON structure is as similar to the original data structures as is realistic.
In addition to its use as a comand line tool, the classes can be used with in-memory data.
This work is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the authors' official duties as a United States Government employee and thus cannot be copyrighted within the United States. The data is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction.
Although all reasonable efforts have been taken to ensure the accuracy and reliability of the data and its source code, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using it. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose.
This code uses the PyBioC library. It can be found at
https://github.com/2mh/PyBioC. Python's sys.path needs to contain
the src directory from where PyBioC was installed. One way to do
this is to modify the pybioc_path line in bioc_json.py. Of course,
there are many other ways to do this.
The script test_bioc_json.sh includes some simple tests to make sure
the code is running properly on your computer.
The json and xml directories contain examples of BioC XML and BioC
JSON files.
./bioc_json.py -b|-j in_file out_file
The option -b means convert to BioC XML, the option -j means convert
to BioC JSON. in_file and out_file are obvious.