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Note : Scrubber 3.X is being ported to Apache cTAKES, this is an interim BETA release. |
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1. Intended usages
1.1 Default configuration
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scrubber.properties : all supported config options and features in one place. Apache UIMA, Apache cTAKES, and WEKA distribution jars are loaded dynamically. |
1.2 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.
2. Software Features
2.1 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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- Compare lexical properties and distributions of public and private text sources
3. How To
3.X Install / Train / Test / Scrub
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4. scrubber.properties
4.1 Java Object
- ScrubberProperties.java statically binds scrubber.properties at startup
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