org.ohnlp.ae.medxn

Class MedNormAnnotator

java.lang.Object

org.apache.uima.analysis_component.AnalysisComponent_ImplBase

org.apache.uima.analysis_component.Annotator_ImplBase

org.apache.uima.analysis_component.JCasAnnotator_ImplBase

org.ohnlp.ae.medxn.MedNormAnnotator

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

public class MedNormAnnotator
extends org.apache.uima.analysis_component.JCasAnnotator_ImplBase

Normalize medication description string same as the RxNorm standard

Author:

Sunghwan Sohn

Constructor Summary

Constructors

Constructor and Description
MedNormAnnotator()

Method Summary

Modifier and Type	Method and Description
protected String	normalizeDrug(Medication med, org.apache.uima.jcas.cas.FSArray attrs) Return a normalized form of RxNorm for med eg) For a given medication information "Fluoxetine [Prozac] 4 MG/ML Oral Solution" Return "fluoxetine4 mg/mloral solutionprozac"
void	process(org.apache.uima.jcas.JCas jcas)

Methods inherited from class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

getRequiredCasInterface, process

Methods inherited from class org.apache.uima.analysis_component.Annotator_ImplBase

getCasInstancesRequired, hasNext, next

Methods inherited from class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

batchProcessComplete, collectionProcessComplete, destroy, getContext, getResultSpecification, initialize, reconfigure, setResultSpecification

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MedNormAnnotator

public MedNormAnnotator()

Method Detail

process

public void process(org.apache.uima.jcas.JCas jcas)
             throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Specified by:

process in class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

normalizeDrug

protected String normalizeDrug(Medication med,
                               org.apache.uima.jcas.cas.FSArray attrs)

Return a normalized form of RxNorm for med eg) For a given medication information "Fluoxetine [Prozac] 4 MG/ML Oral Solution" Return "fluoxetine4 mg/mloral solutionprozac"

Parameters:

med - ConceptMention medication

attrs - medication attributes in FSArray

Returns:

normalized medication information to the RxNorm standard