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

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

Nested Class Summary

Nested classes/interfaces inherited from class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl

BaseLookupConsumerImpl.LookupHitKey

Field Summary

Fields

Modifier and Type	Field and Description
protected Properties	props

Constructor Summary

Constructors

Constructor and Description
UmlsToSnomedConsumerImpl(org.apache.uima.UimaContext aCtx, Properties properties)

Method Summary

Modifier and Type	Method and Description
void	consumeHits(org.apache.uima.jcas.JCas jcas, Iterator<LookupHit> lhItr) Consumes the hits produced by the LookupAnnotator.
protected abstract Set<String>	getSnomedCodes(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

createLookupHitMap, organizeByOffset

Methods inherited from class java.lang.Object

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

Field Detail

props

protected Properties props

Constructor Detail

UmlsToSnomedConsumerImpl

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

Throws:

Exception

Method Detail

getSnomedCodes

protected abstract Set<String> getSnomedCodes(String umlsCode)
                                       throws 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

SQLException

DictionaryException

consumeHits

public void consumeHits(org.apache.uima.jcas.JCas jcas,
                        Iterator<LookupHit> lhItr)
                 throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

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

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