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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
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We recommend starting with the default properties and prebuilt train/test models. |
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).
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scrubber.properties : all supported config options and features in one place. |
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.
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- 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.
Software Features
Annotation
- 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 sets containing lexical properties, medical concept codes, and human defined rules
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- Distinguish (classify) private patient data from coded medical concepts and commonly used words words
Compare
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Text
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Compare lexical properties and distributions of public and private text sources
How-To Guide
Installation
Train and test models
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Install / Train / Test / Scrub
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Scrubber Property KEY = VALUE
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scrubber.properties
*ScrubberProperties.java statically binds scrubber.properties at startup
- ScrubberPropertiesTest.java demonstrates binding scrubber.properties to shell commands.
- TemplateFileProcessor.java IO and token replacement of default configuration files
- setClassPath.sh sets the java classpath and exports the shell variables