org.apache.ctakes.ytex.uima.annotators

Class MetaMapToCTakesAnnotator

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.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

@PipeBitInfo(name="Metamap Annotation xlater",
             description="Create MedicationEventMention/EntityMention annotations for each set of CandidateConcept annotations that span the same text.",
             role=SPECIAL,
             products=IDENTIFIED_ANNOTATION)
public class MetaMapToCTakesAnnotator
extends org.apache.uima.analysis_component.JCasAnnotator_ImplBase

Convert metamap concepts to ctakes named entities.

Create MedicationEventMention/EntityMention annotations for each set of CandidateConcept annotations that span the same text.

if checkMedications is set to true, see if a named entity has a medication semantic type. if so, create a MedicationEventMention. else create EntityMention.

Author:

vijay

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MetaMapToCTakesAnnotator.NegSpan

Constructor Summary

Constructors

Constructor and Description
MetaMapToCTakesAnnotator()

Method Summary

Modifier and Type	Method and Description
void	initialize(org.apache.uima.UimaContext aContext)
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, reconfigure, setResultSpecification

Methods inherited from class java.lang.Object

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

Constructor Detail

MetaMapToCTakesAnnotator

public MetaMapToCTakesAnnotator()

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

initialize

public void initialize(org.apache.uima.UimaContext aContext)
                throws org.apache.uima.resource.ResourceInitializationException

Specified by:

initialize in interface org.apache.uima.analysis_component.AnalysisComponent

Overrides:

initialize in class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

Throws:

org.apache.uima.resource.ResourceInitializationException