org.apache.ctakes.ytex.uima.annotators

Class SenseDisambiguatorAnnotator

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.SenseDisambiguatorAnnotator

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

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

Disambiguate named entities via adapated Lesk algorithm with semantic similarity. Configuration parameters set in ytex.properties / via -D option / in config for SenseDisambiguatorAnnotator (minus the 'ytex.' prefix)

• ytex.sense.windowSize - context window size. concepts from named entities +- windowSize around the target named entity are used for disambiguation. defaults to 10
• ytex.sense.metric - measure to use. defaults to INTRINSIC_PATH
• ytex.conceptGraph - concept graph to use.
• ytex.conceptProperty - field of ontology concept to use. Use cui for UmlsConcept, code for OntologyConcept.

Author:

vijay

Constructor Summary

Constructors

Constructor and Description
SenseDisambiguatorAnnotator()

Method Summary

Modifier and Type	Method and Description
protected void	disambiguate(org.apache.uima.jcas.JCas jcas, List<IdentifiedAnnotation> listNE)
protected String	getConceptId(org.apache.uima.cas.FeatureStructure oc) get the concept id for the specified concept.
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

SenseDisambiguatorAnnotator

public SenseDisambiguatorAnnotator()

Method Detail

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

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

getConceptId

protected String getConceptId(org.apache.uima.cas.FeatureStructure oc)
                       throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

get the concept id for the specified concept. if conceptProperty is defined, get that property. for UmlsConcept, return cui for OntologyConcept, return code

Parameters:

oc -

Returns:

Throws:

IllegalAccessException

ReflectiveOperationException

NoSuchMethodException

org.apache.uima.analysis_engine.AnalysisEngineProcessException

disambiguate

protected void disambiguate(org.apache.uima.jcas.JCas jcas,
                            List<IdentifiedAnnotation> listNE)
                     throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Parameters:

jcas -

listNE - list of named entities to disambiguate

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException