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pyConTextNLP

This package has been in de facto retirement for many years. The direct successor to this project is MedSpaCy.

This code has been validated using the included notebooks on Python v 3.7.2. Python 2.x is no longer supported.

pyConTextNLP is a Python implementation/extension/modification of the ConText algorithm described in "Context: An Algorithm for Determining Negation, Experiencer, and Temporal Status from Clinical Reports" which is itself a generalization of the NegEx algorithm described in "A simple algorithm for identifying negated findings and diseases in discharge summaries".

The package is maintained by Brian Chapman at the University of Utah. Other active and past developers include:

  • Wendy W. Chapman
  • Glenn Dayton
  • Danielle Mowery

Introduction

pyConTextNLP is a partial implementation of the ConText algorithm using Python. The original description of pyConTextNLP was provided in Chapman BE, Lee S, Kang HP, Chapman WW, "Document-level classification of CT pulmonary angiography reports based on an extension of the ConText algorithm." J Biomed Inform. 2011 Oct;44(5):728-37

Other publications/presentations based on pyConText include: * Wilson RA, et al. "Automated ancillary cancer history classification for mesothelioma patients from free-text clinical reports." J Pathol Inform. 2010 Oct 11;1:24. * Chapman BE, Lee S, Kang HP, Chapman WW. "Using ConText to Identify Candidate Pulmonary Embolism Subjects Based on Dictated Radiology Reports." (Presented at AMIA Clinical Research Informatics Summit 2011) * Wilson RA, Chapman WW, DeFries SJ, Becich MJ, Chapman BE. "Identifying History of Ancillary Cancers in Mesothelioma Patients from Free-Text Clinical Reports." (Presented at AMIA 2010).

Note: we changed the package name from pyConText to pyConTextNLP because of a name conflict on pypi.

Installation

Latest Version

The latest version of pyConTextNLP is available on [github](https://github.com/chapmanbe/pyConTextNLP). The package can be installed by either cloning the repository and running python setup.py install. Alternatively or by .. code:: shell

pip install git+https://github.com/chapmanbe/pyConTextNLP.git

PyPi

pyConTextNLP is also available via the Python Package Index and can be installed via

pip install pyConTextNLP

Dependencies include

  • networkx
  • PyYAML

Tutorials

See the notebooks folder for a series of walkthroughs demonstrating pyConTextNLP core concepts with example data.

How to Use

I am working on improving the documentation and (hopefully) adding some testing to the code.

Some preliminary comments:

  • pyConTextNLP works marks up text on a sentence by sentence level.
  • pyConTextNLP assumes the sentence is a string not a list of words
  • Our preferred way to represent knowledge is now with YAML files rather than TSV files.