Hi All,
I have been trying to set up cTakes ( user installation ) with UMLS for
quite some time now. I have installed the UMLS 2016 data into an Oracle
data base.
How will I configure the cTakes to use the data from the data base ?
I am trying to use AggregatePlaintextUMLSProcessor. I read that I need
to configure LookupDesc_Db.xml. Please find attached the file I am
using.
Can somebody please help me out with a step-by-step instructions ?
Thanks,
Vivek Venugopa
Developer | Masonic Cancer Center
<?xml version="1.0" encoding="UTF-8"?>
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<lookupSpecification>
<!-- Defines what dictionaries will be used in terms of implementation specifics and metaField configuration. -->
<dictionaries>
<dictionary id="DICT_UMLS_MS" externalResourceKey="DbConnection" caseSensitive="false">
<implementation>
<jdbcImpl tableName="umls"/>
</implementation>
<lookupField fieldName="fword"/>
<metaFields>
<metaField fieldName="cui"/>
<metaField fieldName="tui"/>
<metaField fieldName="text"/>
</metaFields>
</dictionary>
<dictionary id="DICT_RXNORM" externalResourceKey="RxnormIndexReader" caseSensitive="false">
<implementation>
<jdbcImpl tableName="umls_ms_2011ab_rxnorm"/>
</implementation>
<lookupField fieldName="fword"/>
<metaFields>
<metaField fieldName="cui"/>
<metaField fieldName="tui"/>
<metaField fieldName="text"/>
</metaFields>
</dictionary>
</dictionaries>
<!-- Binds together the components necessary to perform the complete lookup logic start to end. -->
<lookupBindings>
<lookupBinding>
<dictionaryRef idRef="DICT_UMLS_MS"/>
<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl">
<properties>
<property key="textMetaFields" value="text"/>
<property key="maxPermutationLevel" value="7"/>
<!-- <property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.Sentence"/> -->
<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>
<property key="exclusionTags" value="VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,IN,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB"/>
</properties>
</lookupInitializer>
<lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl">
<properties>
<property key="codingScheme" value="SNOMED"/>
<property key="cuiMetaField" value="cui"/>
<property key="tuiMetaField" value="tui"/>
<property key="anatomicalSiteTuis" value="T021,T022,T023,T024,T025,T026,T029,T030"/>
<property key="procedureTuis" value="T059,T060,T061"/>
<property key="disorderTuis" value="T019,T020,T037,T046,T047,T048,T049,T050,T190,T191"/>
<property key="findingTuis" value="T033,T034,T040,T041,T042,T043,T044,T045,T046,T056,T057,T184"/>
<property key="dbConnExtResrcKey" value="DbConnection"/>
<property key="mapPrepStmt" value="select code from mrconso where cui=?"/>
</properties>
</lookupConsumer>
</lookupBinding>
<lookupBinding>
<dictionaryRef idRef="DICT_RXNORM"/>
<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl">
<properties>
<property key="textMetaFields" value="text"/>
<property key="maxPermutationLevel" value="7"/>
<!-- <property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.Sentence"/> -->
<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>
<property key="exclusionTags" value="VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,IN,LS,MD,PDT,POS,PP,PP$,RP,TO,WDT,WP,WPS,WRB"/>
</properties>
</lookupInitializer>
<lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl">
<properties>
<property key="codingScheme" value="RXNORM"/>
<property key="cuiMetaField" value="cui"/>
<property key="tuiMetaField" value="tui"/>
<property key="medicationTuis" value="T073,T103,T109,T110,T111,T115,T121,T122,T123,T130,T168,T192,T195,T197,T200,T203"/>
<property key="dbConnExtResrcKey" value="OrangeBookIndexReader"/>
<property key="mapPrepStmt" value="select CODERXNORM from ORANGE_BOOK where CODE=?"/>
</properties>
</lookupConsumer>
</lookupBinding>
</lookupBindings>
</lookupSpecification>
