semvec/pypi-packages huggingface dataset:
StructuRX 0.2
Interpret medication prescriptions into a structured format using dependency parses or third-party drug NER pipeline
License: Apache 2.0

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.
ClearWrap 0.2
Wrapper for ClearParser
License: Apache 2.0

Wrappers for the `NICTA fork <https://bitbucket.org/nicta_biomed/clearparser_flex>`_
of `ClearParser <https://code.google.com/p/clearparser>`_ dependency parser
allowing customisation of the parsing process. It was developed primarily for the
`StructuRX <https://bitbucket.org/nicta_biomed/structurx>`_ prescription 
interpretation tool.

Certain features also work with the regular unforked ClearParser but this is
very much untested. 

To use this code an installation of ClearParser must be present on your system.

Usage example, if ClearParser is installed to `/usr/local/clearparser`::

 >>> from clearparser import ClearWrapper
 >>> wrapper = ClearWrapper('parsing-config.xml', 'pos-tagging-config.xml', 
 ... 'dep-model.jar', '/usr/local/clearparser')
 >>> sentences = ['I ran']
 >>> parsed = wrapper.parse_in_bulk(sentences)