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Note : Scrubber 3.X is being ported to Apache cTAKES, this is an interim BETA release.

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Intended usages

We recommend starting with the default properties and the prebuilt train/test models.
The train and test models are anonymized feature sets (not text) generated by scrubber runtime.
scrubber.properties : all supported config options and features in one place.
Apache UIMA, Apache cTAKES, and WEKA distribution jars are loaded dynamically.


Default configuration

Developers can use Scrubber 3.X in "default mode" with the same settings as the provided train and test model files. Input and output settings are managed in scrubber.properties (file paths, database settings, method implementations).

Customize NLP pipeline

Scrubber uses Apache UIMA and Apache cTAKES packages, which together provide the NLP pipeline for lexical parsing and medical concept annotation. Generated feature sets are exported to the SQL database or model file (CSV, ARFF). The UIMA and cTAKES services used by Scrubber are defined and configured using scrubber.properties.

Customize Classifier

Scrubber can use different classifier implementations without recompiling the software.
By default scrubber dynamically loads the popular WEKA C4.5 decision tree classifier with multi-class support.



Features


  • Annotate word tokens and redact PHI from physician notes
  • cTAKES lexical parsing and medical dictionary annotation
  • WEKA multi-class decision tree classifier (plugin default)
  • Protege UI support for human expert curators (reads output)
  • Generate feature set of lexical properties, medical concept codes, and human defined rules
  • Compare lexical properties of public and private text sources
  • Distinguish private patient data from coded medical concepts and commonly used words
  • Prebuilt train and test models can be imported to Weka (default), Matlab, or R
  • (default) Test your local physician notes without retraining
  • (optional) retrain model using local physician note samples, publications, and medical dictionaries

How-To Guide

Install
Train
Test
Scrub
Configure

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Scrubber Property KEY = VALUE 



scrubber.properties

  • ScrubberProperties.java statically binds scrubber.properties at startup
  • ScrubberPropertiesTest.java demonstrates binding scrubber.properties to shell commands.
  • setClassPath.sh sets the java classpath and exports the shell variables
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