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Overview of Side Effect

The side effect extraction system extracts physician-asserted drug side effects from clinical notes. Alternatively the system can extract sentences that possibly contain both side effects and causative drugs, which cover higher number of side effect occurrences but needs human validation to extract individual causative drugs and side effects.

Analysis engines (Annotator) Descriptors

SideEffectAggregateTAE.xml

An aggregated engine defines a pipeline used by side effect extraction on plain text with Mayo format section tags.

SideEffectAggregate_CDA_TAE.xml

An aggregated engine defines a pipeline used by side effect extraction on CDA documents.

SideEffectSentenceAggregateTAE.xml

An aggregated engine defines a pipeline used by side effect sentence extraction on plain text with Mayo format section tags.

SideEffectSentenceAggregate_CDA_TAE.xml

An aggregated engine defines a pipeline used by side effect sentence extraction on CDA documents.

SideEffectAnnotator.xml

This annotator uses pattern matching rules to identify side effect and causative drug.
Parameters

Resources
sideEffectDic: - A:: dictionary file that contains the drug and known side effect used for the dictionary lookup rule. The default file includes sample cases

SESentenceClassifierAnnotator.xml

An annotator to extract sentences that contains side effect and causative drugs.
Parameters
PathOfModel - A machine learning model of side effect sentence classification

PSESentenceAnnotator.xml

This annotator extracts spans of sentences that contain potential side effects (i.e., signs/symptoms and diseases/disorders) and drugs and add them to the type PSESentence. Note that certain sections (in clinical notes) defined in parameter, SectionsToIgnore are ignored.
Parameters
SectionToIgnore: sections not to be considered for this annotation (a default one uses Mayo Clinic section convention)

SESentenceFeatureAnnotator.xml

This annotator extracts features for side effect sentence classification and add them to the type PSESentenceFeature.
Parameters
MetaKeywordsFile:
A file of keywords used for side effect sentence classification

LookupWindowAnnotator_sideEffect.xml

A customized lookup window annotator for side effect extraction to properly catch potential side effect candidates.

DictionaryLookupAnnotator_sideEffect.xml

A customized dictionary lookup annotator for side effect extraction.
Resources
LookupDescriptorFile: a lookup descriptor file used for this project
SnomedIndexReader: custom resource specifier
RxnormIndexReader: custom resource specifier
OrangeBookIndexReader: custom resource specifier
CsvSEFile: a file for supplemental named entities. A user may use this file to add extra named entities that are not in a dictionary (the format should be first_word|full_named_entity|typeID(e.g., drug=1, disease/disorder=2, signs/symptoms=3, etc.). The default file includes sample cases.

CAS Consumers

Collection Processing Engine (CPE)

SideEffect_CDA_CPE.xml

A CPE for both side effect and side effect sentence extraction on CDA documents.

SideEffectSentenceCPE.xml

A CPE for both side effect and side effect sentence extraction on plain text with Mayo format section tags.
Resources
libsvm-2.91.jar: The support vector machine (SVM) classification tool used to side effect sentence classification.

Type System - SideEffectTypeSystem.xml

Types used in this project. Click JCasGen to generate necessary types.

How to