StructuRX interprets medication prescriptions into a structured format using
dependency parses [1] or third-party drug NER pipeline [2].

The dependency-parse version uses a hand-crafted set of rules as described in
[1] based on the output of the `ClearParser dependency parser
<https://code.google.com/p/clearparser>`_, while the alternative method
described in [2] uses the output of the drug NER pipeline from the `cTAKES
clinical NER system <http://sourceforge.net/projects/ohnlp/files/cTAKES/>`_.

Created by Andrew MacKinlay from the `Biomedical Informatics team 
<http://nicta.com.au/business/health/biomedical_informatics>`_ at `NICTA 
<http://nicta.com.au>`_, and licensed under the Apache License 2.0.

Recommended installation method:

::

  $ pip install StructuRX

But of course you can instead do an old-fashioned:

::

 $ python setup.py install

from a `VCS checkout <https://bitbucket.org/nicta_biomed/structurx/src>`_ or 
`tarball/zip download <https://bitbucket.org/nicta_biomed/structurx/downloads>`_.
In the latter case you will need to ensure that `ClearWrap 
<https://bitbucket.org/nicta_biomed/clearwrap>`_ is 
installed, and in either case you will need a copy of the 
`NICTA fork <https://bitbucket.org/nicta_biomed/clearparser_flex>`_
of `ClearParser <https://code.google.com/p/clearparser>`_ available to do the
dependency parsing. We highly recommend installing into a virtualenv.
If you wish to test against cTAKES, that will naturally need to be installed as 
well. 

After installing, run the provided script ``structurx-run.py`` and follow
the instructions for configuration.

* [1] A. MacKinlay and K. Verspoor. 2012. `Extracting structured information
  from free-text medication prescriptions using dependencies
  <http://www.nicta.com.au/pub?id=6102>`_. DTMBIO 2012. 
* [2] A. MacKinlay and K.
  Verspoor. 2013. A Comparison of Strategies for Extracting Structured
  Information from Free-Text Medication Prescriptions. LOUHI 2013.

