org.apache.ctakes.dictionary.lookup.ae
Class UmlsToSnomedConsumerImpl

java.lang.Object
  org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl
      org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl

All Implemented Interfaces:

LookupConsumer

Direct Known Subclasses:

UmlsToSnomedDbConsumerImpl, UmlsToSnomedLuceneConsumerImpl

public abstract class UmlsToSnomedConsumerImpl
extends BaseLookupConsumerImpl
implements LookupConsumer

Implementation that takes UMLS dictionary lookup hits and stores as NamedEntity objects only the ones that have a SNOMED synonym. Override abstract method getSnomedCodes and implement looking up the CUI->SNOMED mappings

Author:

Mayo Clinic

Field Summary

protected java.util.Properties

props

Constructor Summary

UmlsToSnomedConsumerImpl(org.apache.uima.UimaContext aCtx, java.util.Properties properties)

Method Summary

void	consumeHits(org.apache.uima.jcas.JCas jcas, java.util.Iterator lhItr) Consumes the hits produced by the LookupAnnotator.
protected abstract java.util.Set	getSnomedCodes(java.lang.String umlsCode) Searches for the Snomed codes that are synonyms of the UMLS concept with CUI umlsCode

Methods inherited from class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl

organizeByOffset

Methods inherited from class java.lang.Object

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

Field Detail

props

protected java.util.Properties props

Constructor Detail

UmlsToSnomedConsumerImpl

public UmlsToSnomedConsumerImpl(org.apache.uima.UimaContext aCtx,
                                java.util.Properties properties)
                         throws java.lang.Exception

Throws:

java.lang.Exception

Method Detail

getSnomedCodes

protected abstract java.util.Set getSnomedCodes(java.lang.String umlsCode)
                                         throws java.sql.SQLException,
                                                DictionaryException

Searches for the Snomed codes that are synonyms of the UMLS concept with CUI umlsCode

Parameters:

umlsCode -

Returns:

Set of SNOMED codes for the given UMLS CUI.

Throws:

SQLException, - DictionaryException

java.sql.SQLException

DictionaryException

consumeHits

public void consumeHits(org.apache.uima.jcas.JCas jcas,
                        java.util.Iterator lhItr)
                 throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Description copied from interface: LookupConsumer

Consumes the hits produced by the LookupAnnotator. This typically means iterating over the hits and storing what's necessary to the JCas

Specified by:

consumeHits in interface LookupConsumer

Specified by:

consumeHits in class BaseLookupConsumerImpl

Parameters:

jcas - CAS for storing data

lhItr - Iterator over LookupHit objects. These objects contain data about the annotation span plus any associated metadata.

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException