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From chen...@apache.org
Subject svn commit: r1588552 [39/42] - in /ctakes/sandbox/ctakes-web-client: ./ .settings/ WebContent/ WebContent/META-INF/ WebContent/WEB-INF/ WebContent/WEB-INF/lib/ src/ src/main/ src/main/java/ src/main/java/org/ src/main/java/org/apache/ src/main/java/org...
Date Fri, 18 Apr 2014 19:48:35 GMT
Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/data/sentenceLevelMetaKeywords.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/data/sentenceLevelMetaKeywords.txt?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/data/sentenceLevelMetaKeywords.txt (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/data/sentenceLevelMetaKeywords.txt Fri Apr 18 19:47:21 2014
@@ -0,0 +1,21 @@
+SideEffectWord|side effect|side effects|side-effect|side-effects|reaction|reactions
+CauseWord|caused|causing|induced|inducing|made|got|resulted|resulting|yielded|yielding
+DueToWord|due to|secondary to|because of|associated with|induced by|attributed to|associate with|associates with|account for|accounts for
+StartVerb|started  
+DiscontVerb|discontinued|stopped
+IncreaseVerb|increased  
+DecreaseVerb|decreased|tapered|lowered  
+NoteVerb|noted|developed|reported|described|had
+AfterDrugWord|after taking|after starting|since
+NoticeVerb|noticed|found
+BecomeVerb|become|became|grew
+FeelWord|feel like|feels like|felt|feeling
+AvoidWord|to avoid
+InitiationNoun|initiation|start
+WithPrep|with
+ForPrep|for
+FromPrep|from
+WhenConj|when
+AfterConj|after
+BecauseConj|because|as    
+HumanSubj|he|she
\ No newline at end of file

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/data/sentenceLevelMetaKeywords.txt
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/LookupDesc_sideEffect.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/LookupDesc_sideEffect.xml?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/LookupDesc_sideEffect.xml (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/LookupDesc_sideEffect.xml Fri Apr 18 19:47:21 2014
@@ -0,0 +1,262 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<lookupSpecification>
+	<!--  Defines what Gazetteers will be used in terms of implementation specifics and metaField configuration. -->
+	<dictionaries>
+		<dictionary id="GAZ_UMLS_MS_2009" externalResourceKey="SnomedIndexReader" caseSensitive="false" cacheDbLookup="true">
+			<implementation>
+				<luceneImpl/>
+			</implementation>
+			<lookupField fieldName="first_word"/>
+			<excludeList>
+			   <child value="does not"/>
+			   <child value="po" />
+			   <child value="dosed" />
+			   <child value="marriage" />
+			   <child value="education" />
+			   <child value="effort" />
+			   <child value="efforts" />
+			   <child value="follow-up" />
+			   <child value="cm"/> 
+			   <child value="w"/>
+			   <child value="k"/>
+         <child value="aid" />
+			   <child value="nearest" />
+			   <child value="near" />
+				<child value="foam" />
+				<child value="pt" />
+				<child value="dr" />
+				<child value="drs" />
+				<child value="md" />
+				<child value="pm" />
+				<child value="is" />
+				<child value="being" />
+				<child value="be" />
+				<child value="mg" />
+				<child value="zinc" />
+				<child value="iron" />
+				<child value="Lead" />
+				<child value="pt" />
+				<child value="symptoms"/>
+				<child value="symptom"/>
+				<child value="problem"/>
+				<child value="problems"/>
+				<child value="drinking"/>
+				<child value="no"/>
+				<child value="discontinued"/>
+				<child value="absence"/>
+				<child value="complaint"/>
+				<child value="complaints"/>
+				<child value="overdose"/>
+				<child value="history"/>
+				<child value="pregnancy"/>
+				<child value="initiation"/>
+			</excludeList>
+			<metaFields>
+				<metaField fieldName="cui"/>
+				<metaField fieldName="tui"/>
+				<metaField fieldName="text"/>
+			</metaFields>
+		</dictionary>
+		<dictionary id="GAZ_RXNORM" externalResourceKey="RxnormIndexReader" caseSensitive="false">
+			<implementation>
+				<luceneImpl/>
+			</implementation>
+			<lookupField fieldName="first_word"/>
+			<excludeList>
+				 <child value="program" />
+			   <child value="today" />
+			   <child value="nicotine" />
+			   <child value="alcohol"/>
+			   <child value="allergies"/>
+			   <child value="factor"/>
+			   <child value="bottle"/>
+			   <child value="bottles"/>
+			   <child value="film"/>
+			   <child value="spray"/>
+			   <child value="sprays"/>
+			   <child value="oil"/>
+			   <child value="oils"/>
+			   <child value="solution"/>
+			   <child value="solutions"/>
+			   <child value="sodium"/>
+			   <child value="syrup"/>
+			   <child value="inhaler"/>
+			   <child value="unit"/>
+			   <child value="units"/>
+			   <child value="cholesterol"/>
+			   <child value="completed"/>
+			   <child value="caplet"/>
+			   <child value="caplets"/>
+			   <child value="chewable"/>
+			   <child value="dose"/>
+			   <child value="doses"/>
+			   <child value="frozen"/>
+			   <child value="freeze"/>
+			   <child value="transdermal patch"/>
+			   <child value="tablet"/>
+			   <child value="tablets"/>
+			   <child value="pack"/>
+			   <child value="packs"/>
+			   <child value="patch"/>
+			   <child value="patches"/>
+			   <child value="pill"/>
+			   <child value="pills"/>
+			   <child value="ointment"/>
+			   <child value="oral"/>
+			   <child value="capsule"/>
+			   <child value="capsules"/>
+			   <child value="cream"/>
+			   <child value="disk"/>
+			   <child value="toothpaste"/>
+			   <child value="topical"/>
+			   <child value="liver"/>
+			   <child value="liquid"/>
+			   <child value="lotion"/>
+			   <child value="lozenge"/>
+			   <child value="lozenges"/>
+			   <child value="nebulizer"/>
+			   <child value="gas"/>
+			   <child value="gel"/>
+			   <child value="prostate"/>
+			   <child value="bar"/>
+			   <child value="be"/>
+			   <child value="being"/>
+			   <child value="cm"/>
+			   <child value="dr"/>
+			   <child value="drs"/>
+			   <child value="is"/>
+			   <child value="urea"/>
+			   <child value="children"/>
+			   <child value="solid"/>
+			   <child value="water"/>
+			   <child value="md"/><child value="pm"/><child value="mg"/><child value="a"/><child value="b"/><child value="c"/><child value="d"/><child value="e"/><child value="f"/><child value="g"/><child value="h"/><child value="i"/><child value="j"/><child value="k"/><child value="l"/><child value="m"/><child value="n"/><child value="o"/><child value="p"/><child value="q"/><child value="r"/><child value="s"/><child value="t"/><child value="q"/><child value="v"/><child value="w"/><child value="x"/><child value="y"/><child value="z"/>
+				<child value="aid" />
+				<child value="nearest" />
+				<child value="near" />
+				<child value="foam" />
+				<child value="pt" />
+				<child value="dr" />
+				<child value="drs" />
+				<child value="is" />
+				<child value="being" />
+				<child value="be" />
+				<child value="air" />
+				<child value="zinc" />
+				<child value="iron" />
+				<child value="Lead" />
+				<child value="foam" />
+				<child value="pt" />
+				<child value="ms" />
+			</excludeList>
+			<metaFields>
+				<metaField fieldName="code"/>
+				<metaField fieldName="codeRxNorm"/>
+				<metaField fieldName="preferred_designation"/>
+				<metaField fieldName="other_designation"/>
+				<metaField fieldName="databaseVersion"/>
+				<metaField fieldName="ndfrtClass1"/>
+				<metaField fieldName="ndfrtClass2"/>
+			</metaFields>
+		</dictionary>
+		<!-- Supplement Terms for the side effect project -->
+		<dictionary id="GAZ_CSV_SE" externalResourceKey="CsvSE" caseSensitive="false">
+		<implementation>
+			<csvImpl delimiter="|" indexedFieldNames="0"/>
+		</implementation>
+		<lookupField fieldName="0"/>
+		<metaFields>
+			<metaField fieldName="1"/>
+			<metaField fieldName="typeId"/>
+		</metaFields>
+		</dictionary>			
+	</dictionaries>
+	
+	<!-- Binds together the components necessary to perform the complete lookup logic start to end. -->
+	<lookupBindings>
+		<lookupBinding>
+			<dictionaryRef idRef="GAZ_UMLS_MS_2009"/>
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl">
+				<properties>
+					<property key="textMetaFields" value="text"/>
+					<property key="maxPermutationLevel" value="5"/>
+					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>
+					<property key="exclusionTags" value="AUX,AUXD,AUXG,AUXN,AUXP,AUXZ,CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB"/>
+				</properties>
+			</lookupInitializer>
+			<lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl">
+				<properties>
+					<property key="codingScheme" value="SNOMED"/>
+					<property key="cuiMetaField" value="cui"/>
+					<property key="tuiMetaField" value="tui"/>
+					<property key="cuiMappingField" value="cui"/>
+					<property key="snomedCodeMappingField" value="code"/>
+					<!-- the following values are used as TUIs for testing: T_AS, T_PR, T_DD, T_SS -->
+					<property key="anatomicalSiteTuis" value="T021,T022,T023,T024,T025,T026,T029,T030,T_AS"/>
+					<property key="procedureTuis" value="T059,T060,T061,T_PR"/>
+					<property key="disorderTuis" value="T019,T020,T037,T046,T047,T048,T049,T050,T190,T191,T_DD"/>
+					<property key="findingTuis" value="T033,T034,T040,T041,T042,T043,T044,T045,T046,T056,T057,T184,T_SS"/>
+					<property key="luceneFilterExtResrcKey" value="UmlsIndexReader"/>
+				</properties>
+			</lookupConsumer>
+		</lookupBinding>
+		<lookupBinding>
+			<dictionaryRef idRef="GAZ_RXNORM"/>
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl">
+				<properties>
+					<property key="textMetaFields" value="preferred_designation|other_designation"/>
+					<property key="maxPermutationLevel" value="5"/>
+					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation"/>
+					<property key="exclusionTags" value="AUX,AUXD,AUXG,AUXN,AUXP,AUXZ,CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,RP,TO,WDT,WP,WPS,WRB"/>
+				</properties>
+			</lookupInitializer>
+			<lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl">
+				<properties>
+					<property key="codingScheme" value="RXNORM"/>
+					<property key="codeMetaField" value="code"/>
+					<property key="codeMetaRxField" value="codeRxNorm"/>
+					<property key="databaseVersion" value="RXN2009"/>
+					<property key="primaryClassification" value="ndfrtClass1"/>
+					<property key="secondaryClassification" value="ndfrtClass2"/>
+					<property key="luceneFilterExtResrcKey" value="NamedEntityLookupConsumer"/>
+				</properties>
+			</lookupConsumer>
+		</lookupBinding>
+		<!-- Supplement Terms for the side effect project -->
+		<lookupBinding>
+			<dictionaryRef idRef="GAZ_CSV_SE"/>												
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl">
+				<properties>
+					<property key="textMetaFields" value="1"/>
+					<property key="maxPermutationLevel" value="5"/>
+					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>		
+				</properties>
+			</lookupInitializer>
+			<lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl">
+				<properties>
+					<property key="codingScheme" value="CT"/>
+					<property key="typeIdField" value="2"/>
+				</properties>
+			</lookupConsumer>
+		</lookupBinding>
+	</lookupBindings>
+</lookupSpecification>

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/LookupDesc_sideEffect.xml
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/LookupDesc_sideEffectUMLS.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/LookupDesc_sideEffectUMLS.xml?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/LookupDesc_sideEffectUMLS.xml (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/LookupDesc_sideEffectUMLS.xml Fri Apr 18 19:47:21 2014
@@ -0,0 +1,263 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<lookupSpecification>
+	<!--  Defines what Gazetteers will be used in terms of implementation specifics and metaField configuration. -->
+	<dictionaries>
+		<dictionary id="DICT_UMLS_MS" externalResourceKey="DbConnection" caseSensitive="false" cacheDbLookup="true">
+			<implementation>
+				<jdbcImpl tableName="umls_ms_2011ab"/>
+			</implementation>
+			<lookupField fieldName="first_word"/>
+			<excludeList>
+			   <child value="does not"/>
+			   <child value="po" />
+			   <child value="dosed" />
+			   <child value="marriage" />
+			   <child value="education" />
+			   <child value="effort" />
+			   <child value="efforts" />
+			   <child value="follow-up" />
+			   <child value="cm"/> 
+			   <child value="w"/>
+			   <child value="k"/>
+         <child value="aid" />
+			   <child value="nearest" />
+			   <child value="near" />
+				<child value="foam" />
+				<child value="pt" />
+				<child value="dr" />
+				<child value="drs" />
+				<child value="md" />
+				<child value="pm" />
+				<child value="is" />
+				<child value="being" />
+				<child value="be" />
+				<child value="mg" />
+				<child value="zinc" />
+				<child value="iron" />
+				<child value="Lead" />
+				<child value="pt" />
+				<child value="symptoms"/>
+				<child value="symptom"/>
+				<child value="problem"/>
+				<child value="problems"/>
+				<child value="drinking"/>
+				<child value="no"/>
+				<child value="discontinued"/>
+				<child value="absence"/>
+				<child value="complaint"/>
+				<child value="complaints"/>
+				<child value="overdose"/>
+				<child value="history"/>
+				<child value="pregnancy"/>
+				<child value="initiation"/>
+			</excludeList>
+			<metaFields>
+				<metaField fieldName="cui"/>
+				<metaField fieldName="tui"/>
+				<metaField fieldName="text"/>
+			</metaFields>
+		</dictionary>
+		<dictionary id="DICT_RXNORM" externalResourceKey="RxnormIndexReader" caseSensitive="false">
+			<implementation>
+				<luceneImpl/>
+			</implementation>
+			<lookupField fieldName="first_word"/>
+			<excludeList>
+				 <child value="program" />
+			   <child value="today" />
+			   <child value="nicotine" />
+			   <child value="alcohol"/>
+			   <child value="allergies"/>
+			   <child value="factor"/>
+			   <child value="bottle"/>
+			   <child value="bottles"/>
+			   <child value="film"/>
+			   <child value="spray"/>
+			   <child value="sprays"/>
+			   <child value="oil"/>
+			   <child value="oils"/>
+			   <child value="solution"/>
+			   <child value="solutions"/>
+			   <child value="sodium"/>
+			   <child value="syrup"/>
+			   <child value="inhaler"/>
+			   <child value="unit"/>
+			   <child value="units"/>
+			   <child value="cholesterol"/>
+			   <child value="completed"/>
+			   <child value="caplet"/>
+			   <child value="caplets"/>
+			   <child value="chewable"/>
+			   <child value="dose"/>
+			   <child value="doses"/>
+			   <child value="frozen"/>
+			   <child value="freeze"/>
+			   <child value="transdermal patch"/>
+			   <child value="tablet"/>
+			   <child value="tablets"/>
+			   <child value="pack"/>
+			   <child value="packs"/>
+			   <child value="patch"/>
+			   <child value="patches"/>
+			   <child value="pill"/>
+			   <child value="pills"/>
+			   <child value="ointment"/>
+			   <child value="oral"/>
+			   <child value="capsule"/>
+			   <child value="capsules"/>
+			   <child value="cream"/>
+			   <child value="disk"/>
+			   <child value="toothpaste"/>
+			   <child value="topical"/>
+			   <child value="liver"/>
+			   <child value="liquid"/>
+			   <child value="lotion"/>
+			   <child value="lozenge"/>
+			   <child value="lozenges"/>
+			   <child value="nebulizer"/>
+			   <child value="gas"/>
+			   <child value="gel"/>
+			   <child value="prostate"/>
+			   <child value="bar"/>
+			   <child value="be"/>
+			   <child value="being"/>
+			   <child value="cm"/>
+			   <child value="dr"/>
+			   <child value="drs"/>
+			   <child value="is"/>
+			   <child value="urea"/>
+			   <child value="children"/>
+			   <child value="solid"/>
+			   <child value="water"/>
+			   <child value="md"/><child value="pm"/><child value="mg"/><child value="a"/><child value="b"/><child value="c"/><child value="d"/><child value="e"/><child value="f"/><child value="g"/><child value="h"/><child value="i"/><child value="j"/><child value="k"/><child value="l"/><child value="m"/><child value="n"/><child value="o"/><child value="p"/><child value="q"/><child value="r"/><child value="s"/><child value="t"/><child value="q"/><child value="v"/><child value="w"/><child value="x"/><child value="y"/><child value="z"/>
+				<child value="aid" />
+				<child value="nearest" />
+				<child value="near" />
+				<child value="foam" />
+				<child value="pt" />
+				<child value="dr" />
+				<child value="drs" />
+				<child value="is" />
+				<child value="being" />
+				<child value="be" />
+				<child value="air" />
+				<child value="zinc" />
+				<child value="iron" />
+				<child value="Lead" />
+				<child value="foam" />
+				<child value="pt" />
+				<child value="ms" />
+			</excludeList>
+			<metaFields>
+				<metaField fieldName="code"/>
+				<metaField fieldName="codeRxNorm"/>
+				<metaField fieldName="preferred_designation"/>
+				<metaField fieldName="other_designation"/>
+				<metaField fieldName="databaseVersion"/>
+				<metaField fieldName="ndfrtClass1"/>
+				<metaField fieldName="ndfrtClass2"/>
+			</metaFields>
+		</dictionary>
+		<!-- Supplement Terms for the side effect project -->
+		<dictionary id="GAZ_CSV_SE" externalResourceKey="CsvSE" caseSensitive="false">
+		<implementation>
+			<csvImpl delimiter="|" indexedFieldNames="0"/>
+		</implementation>
+		<lookupField fieldName="0"/>
+		<metaFields>
+			<metaField fieldName="1"/>
+			<metaField fieldName="typeId"/>
+		</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="5"/>
+					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>
+					<property key="exclusionTags" value="AUX,AUXD,AUXG,AUXN,AUXP,AUXZ,CC,CD,DT,EX,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="cuiMappingField" value="cui"/>
+					<property key="snomedCodeMappingField" value="code"/>
+					<!-- the following values are used as TUIs for testing: T_AS, T_PR, T_DD, T_SS -->
+					<property key="anatomicalSiteTuis" value="T021,T022,T023,T024,T025,T026,T029,T030,T_AS"/>
+					<property key="procedureTuis" value="T059,T060,T061,T_PR"/>
+					<property key="disorderTuis" value="T019,T020,T037,T046,T047,T048,T049,T050,T190,T191,T_DD"/>
+					<property key="findingTuis" value="T033,T034,T040,T041,T042,T043,T044,T045,T046,T056,T057,T184,T_SS"/>
+					<property key="dbConnExtResrcKey" value="DbConnection" /> 
+					<property key="mapPrepStmt" value="select code from umls_snomed_map where cui=?" /> 
+				</properties>
+			</lookupConsumer>
+		</lookupBinding>
+		<lookupBinding>
+			<dictionaryRef idRef="DICT_RXNORM"/>
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl">
+				<properties>
+					<property key="textMetaFields" value="preferred_designation|other_designation"/>
+					<property key="maxPermutationLevel" value="5"/>
+					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation"/>
+					<property key="exclusionTags" value="AUX,AUXD,AUXG,AUXN,AUXP,AUXZ,CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,RP,TO,WDT,WP,WPS,WRB"/>
+				</properties>
+			</lookupInitializer>
+			<lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl">
+				<properties>
+					<property key="codingScheme" value="RXNORM"/>
+					<property key="codeMetaField" value="code"/>
+					<property key="codeMetaRxField" value="codeRxNorm"/>
+					<property key="databaseVersion" value="RXN2009"/>
+					<property key="primaryClassification" value="ndfrtClass1"/>
+					<property key="secondaryClassification" value="ndfrtClass2"/>
+					<property key="luceneFilterExtResrcKey" value="NamedEntityLookupConsumer"/>
+				</properties>
+			</lookupConsumer>
+		</lookupBinding>
+		<!-- Supplement Terms for the side effect project -->
+		<lookupBinding>
+			<dictionaryRef idRef="GAZ_CSV_SE"/>												
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl">
+				<properties>
+					<property key="textMetaFields" value="1"/>
+					<property key="maxPermutationLevel" value="5"/>
+					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>		
+				</properties>
+			</lookupInitializer>
+			<lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl">
+				<properties>
+					<property key="codingScheme" value="CT"/>
+					<property key="typeIdField" value="2"/>
+				</properties>
+			</lookupConsumer>
+		</lookupBinding>
+	</lookupBindings>
+</lookupSpecification>

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/LookupDesc_sideEffectUMLS.xml
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/additionalNE_dictionary.csv
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/additionalNE_dictionary.csv?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/additionalNE_dictionary.csv (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/additionalNE_dictionary.csv Fri Apr 18 19:47:21 2014
@@ -0,0 +1,124 @@
+sulfonamide|sulfonamide|1
+sulfonamides|sulfonamides|1
+nsaids|nsaids|1
+anti-inflam|anti-inflam agent|1
+anti-inflam|anti-inflam agents|1
+anti-inflammatory|anti-inflammatory agent|1
+anti-inflammatory|anti-inflammatory agents|1
+ace|ace inhibitor|1
+ace|ace inhibitors|1
+thiomersal|thiomersal|1
+divalproex|divalproex|1
+acamprosate|acamprosate|1
+quetiapine|quetiapine|1
+
+anti|anti inflam agent|1
+anti|anti inflam agents|1
+anti|anti inflammatory agent|1
+anti|anti inflammatory agents|1
+
+benztropine|benztropine meylate|1
+hydrochloride|hydrochloride|1
+propranolol|propranolol hydrocloride|1
+duloxetine|duloxetine hydrochoride|1
+effexor-xr|effexor-xr|1
+zyban|zyban|1
+ritalin|ritalin sr|1
+doxican|doxican|1
+diclofenac|diclofenac sodium and misoprostol|1
+acetaminophen|acetaminophen and caffeine|1
+Acetaminophen|Acetaminophen and Hydrocodone|1
+fluoxetine|fluoxetine and olanzapine|1
+amphetamine|amphetamine and dextroamphetamine|1
+diclofenac|diclofenac and misoprostol|1
+enovil|enovil|1
+sinquan|sinquan|1
+milnacipran|milnacipran|1
+aponol|aponol|1
+janimine|janimine|1
+revive|revive|1
+cipralex|cipralex|1
+savella|savella|1
+enerjets|enerjets|1
+ixel|ixel|1
+diastat|diastat pediatric|1
+yentreve|yentreve|1
+
+side|side effect|3
+side|side effects|3
+side-effect|side-effect|3
+side-effects|side-effects|3
+sexual|sexual side-effects|3
+sexual|sexual side effects|3
+sexual|sexual side-effect|3
+sexual|sexual side effect|3
+reaction|reaction|3
+weight|weight loss|3
+weight-loss|weight-loss|3
+weight|weight gain|3
+weight-gain|weight-gain|3
+jittery|jittery|3
+sick|sick|3
+
+sweating|sweating increased|3
+ringing|ringing|3
+ringing|ringing in ears|3
+arthralia|arthralia|3
+gas|gas|3
+libido|libido decreased|3
+thirst|thirst|3
+overexcitement|overexcitement|3
+swollen|swollen tongue|3
+trouble|trouble speaking|3
+watery|watery mouth|3
+inability|inability|3
+light-headed|light-headed|3
+vision|vision changes|3
+difficulty|difficulty swallowing|3
+tightness|tightness|3
+heartbeat|heartbeat|3
+heart|heart rate|3
+weakness|weakness|3
+sexual|sexual ability|3
+mental|mental changes|3
+memory|memory loss|3
+black-out|black-out|3
+jitteriness|jitteriness|3
+hurting|hurting|3
+sleep|sleep disturbances|3
+peeling|peeling|3
+breath|breath odor|3
+mental|mental slowness|3
+crying|crying|3
+shakiness|shakiness|3
+problems|problems with urination|3
+vision|vision loss|3
+nipple|nipple discharge|3
+menstrual|menstrual changes|3
+choking|choking|3
+unsteadiness|unsteadiness|3
+weight|weight changes|3
+nervous|nervous|3
+sore|sore throat|3
+aggressiveness|aggressiveness|3
+unsteady|unsteady|3
+bumps|bumps|3
+wheezing|wheezing|3
+sluggish|sluggish|3
+sedation|sedation|3
+sedate|sedate|3
+anergic|anergic|3
+anxious|anxious|3
+panicky|panicky|3
+eye|eye pressure|3
+mood|mood deterioration|3
+diminishment|diminishment|3
+groggy|groggy|3
+suicidal|suicidal thinking|3
+shortness-of-breath|shortness-of-breath|3
+hypomanic|hypomanic|3
+numb|numb|3
+serotonin|serotonin syndrome|3
+cardiac|cardiac|3
+drugged|drugged|3
+intoxicated|intoxicated|3

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/sideEffect_dictionary.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/sideEffect_dictionary.txt?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/sideEffect_dictionary.txt (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/lookup/sideEffect_dictionary.txt Fri Apr 18 19:47:21 2014
@@ -0,0 +1,46 @@
+//FORMAT: generic drug|brand drug|side effect1, side effect2,...
+//removed some paradoxical side effects
+Amitriptyline|Elavil, Enovil|fast heart rate, pounding heart rate, uneven heart rate, chest pain, heavy feeling chest, pain spreading to the arm, pain spreading to the shoulder, nausea, sweating, general ill feeling, sudden numbness, sudden weakness, sudden headache, confusion, problems with vision, problems with speech, problems with balance, hallucinations, seizures, convulsions, feeling light-headed, fainting, restless muscle movements in your eyes, restless muscle movements in your tongue, restless muscle movements in your jaw, restless muscle movements in your neck, uncontrollable shaking, uncontrollable tremor, skin rash, severe tingling, numbness, muscle weakness, easy bruising, easy bleeding, extreme thirst with headache, extreme thirst with nausea, extreme thirst with vomiting, extreme thirst with weakness, urinating less than usual, not urinating at all, nausea, vomiting, constipation, diarrhea, loss of appetite, dry mouth, unpleasant taste, feeling dizzy, feeling drowsy, 
 feeling tired, trouble concentrating, nightmares, blurred vision, headache, ringing in your ears, breast swelling, decreased sex drive, impotence, difficulty having an orgasm
+Bupropion|Wellbutrin, Wellbutrin SR, Zyban|severe blistering, peeling, red skin rash, fever, swollen glands, rash, itching, joint pain, general ill feeling, confusion, trouble concentrating, hallucinations, unusual thoughts, unusual behavior, headache, migraine, sleep problems, nausea, vomiting, constipation, dry mouth, dizziness, tremors, shaking, appetite changes, weight loss, weight gain, mild itching, skin rash, increased sweating, loss of interest in sex
+Buspirone|Buspar|feeling light-headed, fainting, fast heart rate, uneven heart rate, depressed mood, unusual thoughts, unusual behavior, lack of balance, lack of coordination, drowsiness, dizziness, blurred vision, feeling restless, nausea, upset stomach, sleep problems, insomnia, trouble concentrating
+Citalopram|Celexa|very stiff rigid muscles, high fever, sweating, fast heartbeats, uneven heartbeats, tremors, overactive reflexes, nausea, vomiting, diarrhea, loss of appetite, feeling unsteady, loss of coordination, headache, trouble concentrating, memory problems, weakness, confusion, hallucinations, fainting, seizure, shallow breathing, breathing that stops, drowsiness, sleep problems, mild nausea, gas, upset stomach, weight changes, urinating more than usual, decreased sex drive, impotence, difficulty having an orgasm, dry mouth, watery mouth, yawning, cold symptoms such as stuffy nose, sneezing, sore throat
+Clomipramine|Anafranil|Constipation, diarrhea, dizziness, drowsiness, dry mouth, headache, irritability, loss of appetite, nausea, nightmares, sweating, tiredness, upset stomach, vomiting, weakness, weight loss, weight gain, rash, hives, itching, difficulty breathing, tightness in the chest, swelling of the mouth, swelling of the face, swelling of the lips, swelling of the tongue, blurred vision, other vision changes, changes in sex drive, chest pain, confusion, decreased sexual ability, fainting, fast heartbeat, slow heartbeat, irregular heartbeat, fever, flushing, frequent urination, difficult urination, impulsive behavior, unusual changes in behavior, mental changes, mood changes, increased anxiety, mood swings, agitation, irritability, nervousness, restlessness, numbness of the skin, tingling of the skin, panic attacks, ringing in the ears, seizures, severe dizziness, severe drowsiness, sore throat, stomach pain, suicidal thinking, suicidal behavior, swelling of the testicles, t
 remor, trouble sleeping, trouble walking, trouble keeping your balance, twitching of the face, twitching of the tongue, uncontrolled movements of arms, stiffness of arms and legs, unusual bleeding, unusual bruising, worsening of depression, yellowing of the skin, yellowing of eyes
+Desipramine|Norpramin|Blurred vision, change in sexual desire, change in sexual ability, constipation, diarrhea, dizziness, drowsiness, dry mouth, headache, loss of appetite, nausea, tiredness, trouble sleeping, weakness, rash, hives, itching, difficulty breathing, tightness in the chest, swelling of the mouth, swelling of the face, swelling of the lips, swelling of the tongue, chest pain, confusion, dark urine, delusions, difficulty speaking, difficulty swallowing, excessive sweating, fainting, fast heartbeat, irregular heartbeat, fever, chills, sore throat, hallucinations, new agitation, worsening agitation, anxiety, panic attacks, aggressiveness, impulsiveness, irritability, hostility, exaggerated feeling of well-being, restlessness, inability to sit still, numbness in an arm, numbness in a leg, tingling in an arm, tingling in a leg, one-sided weakness, seizures, severe dizziness, persistent dizziness, persistent headache, severe trouble sleeping, persistent trouble sleeping, slu
 rred speech, stiff muscles, suicidal thoughts, suicidal actions, tremor, trouble urinating, uncontrolled muscle movements of face, uncontrolled muscle movements of tongue, uncontrolled muscle movements of arms, uncontrolled muscle movements of legs, unusual bleeding, unusual bruising, unusual mental changes, severe mental changes, unusual mood changes, severe mood changes, vision problems, yellowing of the skin, yellowing of eyes
+Doxepin|Adapin, Aponol, Sinquan, Sinequan|Appetite loss, constipation, diarrhea, dizziness, drowsiness, dry mouth, excess sweating, headache, heartburn, increased appetite, indigestion, nausea, unpleasant taste, urinary retention, vomiting, weakness, weight gain, rash, hives, itching, difficulty breathing, tightness in the chest, swelling of the mouth, swelling of the face, swelling of the lips, swelling of the tongue, abnormal movements, aggressive behavior, bizarre behavior, agitation, anxiety, blurred vision, other vision changes, chest pain, difficulty speaking, difficulty swallowing, disorientation, eye pain, fainting, fast heartbeat, slow heartbeat, irregular heartbeat, hair loss, hallucinations, hostility, irritability, loss of balance, mood swings, nervousness, restlessness, panic attacks, ringing in the ears, seizures, shakiness, sore throat, fever, trouble sleeping, twitching of the face, twitching of the tongue, unusual bleeding, unusual bruising, yellowing of the skin, y
 ellowing of the eyes
+Duloxetine|Cymbalta, Yentreve|nausea, stomach pain, low fever, loss of appetite, dark urine, clay-colored stools, jaundice, yellowing of the skin, yellowing of the eyes, painful urination, difficult urination, easy bruising, easy bleeding, nosebleeds, black stools, bloody stools, tarry stools, very stiff rigid muscles, high fever, vomiting, diarrhea, sweating, fast heartbeats, uneven heartbeats, tremors, overactive reflexes, headache, trouble concentrating, memory problems, confusion, hallucinations, weakness, feeling unsteady, loss of coordination, fainting, seizure, shallow breathing, breathing that stops, dry mouth, blurred vision, drowsiness, dizziness, spinning sensation, mild nausea, constipation, gas, sleep problems, insomnia, joint pain, muscle pain, weight changes, decreased sex drive, impotence, difficulty having an orgasm
+Escitalopram|Lexapro, Cipralex|very stiff rigid muscles, high fever, sweating, fast heartbeats, uneven heartbeats, tremors, overactive reflexes, nausea, vomiting, diarrhea, loss of appetite, feeling unsteady, loss of coordination, headache, trouble concentrating, memory problems, weakness, confusion, hallucinations, fainting, seizure, shallow breathing, breathing that stops, drowsiness, dizziness, sleep problems, insomnia, mild nausea, gas, heartburn, upset stomach, constipation, weight changes, decreased sex drive, impotence, difficulty having an orgasm, dry mouth, yawning, ringing in your ears
+//Flibanserin|Not FDA approved in US| - N/A in drugs.com 
+Fluoxetine|prozac|severe blistering, peeling, red skin rash, very stiff rigid muscles, high fever, sweating, fast heartbeats, uneven heartbeats, tremors, overactive reflexes, nausea, vomiting, diarrhea, loss of appetite, feeling unsteady, loss of coordination, headache, trouble concentrating, memory problems, weakness, confusion, hallucinations, fainting, seizure, shallow breathing, breathing that stops, cold symptoms such as stuffy nose, sneezing, sore throat, drowsiness, dizziness, feeling nervous, mild nausea, upset stomach, constipation, increased appetite, weight changes, sleep problems, insomnia, decreased sex drive, impotence, difficulty having an orgasm, dry mouth
+Fluvoxamine|Luvox|Constipation, decreased sexual ability, diarrhea, dizziness, drowsiness, dry mouth, gas, headache, increased sweating, loss of appetite, nausea, nervousness, sore throat, stomach upset, trouble sleeping, vomiting, weakness, rash, hives, itching, difficulty breathing, tightness in the chest, swelling of the mouth, swelling of the face, swelling of the lips, swelling of the tongue, bizarre behavior, black stools, bloody stools, chest pain, confusion, decreased concentration, decreased coordination, exaggerated reflexes, fainting, fast heartbeat, irregular heartbeat, fever, hallucinations, memory loss, new agitation, worsening agitation, panic attacks, aggressiveness, impulsiveness, irritability, hostility, exaggerated feeling of well-being, restlessness, inability to sit still, painful menstrual periods, persistent erection, painful erection, red skin, swollen skin, blistered skin, peeling skin, seizures, severe headache, persistent headache, trouble sleeping, stiff 
 muscles, stomach pain, suicidal thoughts, suicidal attempts, tremor, unusual bruising, unusual bleeding, unusual mental changes, severe mental changes, unusual mood changes, severe mood changes, unusual swelling, unusual weakness, vision changes
+Imipramine|Janimine, Tofranil|Dizziness, drowsiness, dry mouth, excitement, headache, impotence, nausea, nightmares, pupil dilation, sensitivity to sunlight, sweating, tiredness, upset stomach, vomiting, weakness, weight loss, weight gain, rash, hives, itching, difficulty breathing, tightness in the chest, swelling of the mouth, swelling of the face, swelling of the lips, swelling of the tongue, blurred vision, other vision changes, changes in sex drive, chest pain, confusion, constipation, fainting, fast heartbeat, slow heartbeat, irregular heartbeat, fever, frequent urination, difficult urination, hallucinations, impulsive behavior, other unusual changes in behavior jaw spasms, neck spasms, muscle spasms, mental changes, mood changes, increased anxiety, mood swings, agitation, irritability, nervousness, restlessness, panic attacks, ringing in the ears, seizures, severe dizziness, drowsiness, sore throat, stomach pain, suicidal thinking, suicidal behavior, swelling of the testicles
 , tremor, trouble sleeping, trouble walking, trouble keeping your balance, twitching of the face, twitching of the tongue, uncontrolled movements of arms and legs, stiffness, unusual bleeding, unusual bruising, worsening of depression, yellowing of the skin, yellowing of the eyes
+Milnacipran|Ixel, Savella|fast heartbeats, pounding heartbeats, painful urination, difficult urination, easy bruising, easy bleeding, nosebleeds, bloody stools, tarry stools, coughing up blood, confusion, hallucinations, severe weakness, seizure, convulsions, high fever, sweating, chills, goose bumps, memory problems, trouble concentrating, loss of coordination, overactive reflexes, vomiting, diarrhea, high blood pressure, severe headache, blurred vision, buzzing in your ears, chest pain, shortness of breath, uneven heartbeats, stomach pain, loss of appetite, dark urine, clay-colored stools, jaundice, yellowing of the skin, yellowing of the eyes, constipation, dry mouth, nausea, stomach pain, heartburn, bloating, dizziness, drowsiness, headache, tired feeling, stuffy nose, sneezing, other cold symptoms, sleep problems, insomnia, swelling in your hands, swelling in your feet, hot flashes, sweating, itching, mild skin rash, numbness, tingling, blurred vision, decreased sex drive, impo
 tence, difficulty having an orgasm
+Mirtazapine|Remeron|fever, chills, body aches, flu symptoms, white patches inside your mouth, sores inside your mouth, sores on your lips, feeling like you might pass out, drowsiness, dizziness, weakness, nausea, stomach pain, constipation, increased appetite, weight gain, dry mouth, thirst
+//Moclobemide|Aurorix, Manerix| - N/A in drugs.com 
+Nefazodone|Serzone|difficulty breathing, closing of your throat, swelling of your lips, swelling of your tongue, swelling of your face, hives, fainting, prolonged erection, painful erection, inappropriate erections, dizziness, lightheadedness, drowsiness, upset stomach, insomnia, dry mouth, constipation, blurred vision, abnormal vision
+Nortriptyline|Aventyl, Pamelor|Dizziness, drowsiness, dry mouth, excitement, headache, impotence, nausea, nightmares, pupil dilation, sensitivity to sunlight, sweating, tiredness, upset stomach, vomiting, weakness, weight loss, weight gain, rash, hives, itching, difficulty breathing, tightness in the chest, swelling of the mouth, swelling of the face, swelling of the lips, swelling of the tongue, blurred vision, other vision changes, changes in sex drive, chest pain, confusion, constipation, fainting, fast heartbeat, slow heartbeat, irregular heartbeat, fever, frequent urination, difficult urination, hallucinations, impulsive behavior, other unusual changes in behavior, jaw spasms, neck spasms, muscle spasms, mental changes, mood changes, increased anxiety, mood swings, agitation, irritability, nervousness, restlessness, panic attacks, ringing in the ears, seizures, severe dizziness, severe drowsiness, sore throat, stomach pain, suicidal thinking, suicidal behavior, swelling of the 
 testicles, tremor, trouble sleeping, trouble walking, trouble keeping your balance, twitching of the face, twitching of the tongue, uncontrolled movements of arms and legs, stiffness, unusual bleeding, unusual bruising, worsening of depression, yellowing of the skin, yellowing of the eyes
+Paroxetine|Paxil|easy bruising, easy bleeding, nosebleed, very stiff rigid muscles, high fever, sweating, fast heartbeats, uneven heartbeats, tremors, overactive reflexes, nausea, vomiting, diarrhea, loss of appetite, feeling unsteady, loss of coordination, headache, trouble concentrating, memory problems, weakness, confusion, hallucinations, fainting, seizure, shallow breathing, breathing that stops, feeling nervous, drowsiness, dizziness, sleep problems, insomnia, mild nausea, constipation, weight changes, decreased sex drive, impotence, difficulty having an orgasm, dry mouth, yawning, ringing in your ears
+Sertraline|Zoloft|very stiff rigid muscles, high fever, sweating, fast heartbeats, uneven heartbeats, tremors, overactive reflexes, nausea, vomiting, diarrhea, loss of appetite, feeling unsteady, loss of coordination, headache, trouble concentrating, memory problems, weakness, confusion, hallucinations, fainting, seizure, shallow breathing, breathing that stops, drowsiness, dizziness, tired feeling, mild nausea, stomach pain, upset stomach, constipation, dry mouth, changes in appetite, changes in weight, sleep problems, insomnia, decreased sex drive, impotence, difficulty having an orgasm
+Trazodone|Desyrel|Blurred vision, constipation, decreased appetite, dizziness, drowsiness, dry mouth, general body discomfort, headache, incoordination, light-headedness, muscle aches, muscle pains, nausea, nervousness, sleeplessness, stomach pain, stuffy nose, swelling of the skin, tiredness, tremors, rash, hives, itching, difficulty breathing, tightness in the chest, swelling of the mouth, swelling of the face, swelling of the lips, swelling of the tongue, blood in urine, chest pain, fainting, hallucinations, irregular heartbeat, light-headedness when rising from a lying position, light-headedness when rising from a seated position, prolonged erections, inappropriate erections, painful erections, seizures, shortness of breath, stroke, vomiting
+Venlafaxine|Effexor, Effexor-XR|increased blood pressure, severe headache, blurred vision, easy bruising, easy bleeding, severe blistering, peeling skin, red skin rash, very stiff rigid muscles, high fever, sweating, fast heartbeats, uneven heartbeats, tremors, overactive reflexes, nausea, vomiting, diarrhea, loss of appetite, feeling unsteady, loss of coordination, headache, trouble concentrating, memory problems, weakness, confusion, hallucinations, fainting, seizure, shallow breathing, breathing that stops, drowsiness, dizziness, feeling nervous, dry mouth, mild nausea, constipation, decreased sex drive, impotence, difficulty having an orgasm, blurred vision, increased appetite, changes in weight
+Aripiprazole|Abilify|fever, stiff muscles, confusion, sweating, fast heartbeats, uneven heartbeats, jerky muscle movements you cannot control, sudden numbness, sudden weakness, headache, confusion, problems with vision, problems with speech, problems with balance, fever, chills, body aches, flu symptoms, white patches inside your mouth, sores inside your mouth, sores on your lips, increased thirst, increased urination, loss of appetite, fruity breath odor, drowsiness, dry skin, nausea, vomiting, seizure, convulsions, thoughts of hurting yourself, feeling like you might pass out, jaundice, yellowing of your skin, yellowing of your eyes, urinating less than usual, not urinating at all, choking, trouble swallowing, dizziness, drowsiness, weakness, constipation, mild stomach upset, headache, sleep problems, insomnia, weight gain
+Chlorpromazine|Thorazine|Agitation, dizziness, drowsiness, dry mouth, enlarged pupils, jitteriness, nausea, stuffy nose, rash, hives, itching, difficulty breathing, tightness in the chest, swelling of the mouth, swelling of the face, swelling of the lips, swelling of the tongue, changes in menstrual period, changes in sexual ability, dark urine, difficulty swallowing, drooling, fainting, fast heartbeat, irregular heartbeat, fever, chills, sore throat, involuntary movements, involuntary spasms of the arms and legs, involuntary spasms of the tongue, involuntary spasms of the  face, involuntary spasms of the mouth, involuntary spasms of the jaw, mask-like face, muscle restlessness, prolonged errection, painful erection, restlessness, seizures, shuffling walk, sleeplessness, stiff muscles, rigid muscles, stomach pain, sweating, trouble urinating, unusual eye movements, inability to move eyes, unusual mood, unusual mental changes, lack of response to your surroundings, vision changes, we
 akness of arms, weakness of legs, yellowing of the skin, yellowing of the eyes
+Clozapine|Clozaril|feeling short of breath, feeling short of breath even at night, feeling short of breath with mild exertion, swelling in your hands, swelling in your feet, fever, weakness, sore throat, stiff muscles, confusion, sweating, fast heartbeats, uneven heartbeats, sudden numbness, sudden weakness, sudden numbness on one side of the body, sudden weakness on one side of the body, sudden headache, confusion, problems with vision, problems with speech, problems with balance, chest pain, sudden cough, wheezing, rapid breathing, fast heart rate, pain in one, pain in both legs, swelling in one leg, swelling in both legs, white patches inside your mouth, sores inside your mouth, sores on your lips, nausea, vomiting, loss of appetite, jaundice, yellowing of your skin, yellowing of your eyes, seizure, black-out, convulsions, constipation, drooling, increased sweating, drowsiness, dizziness, spinning sensation, sleep problems, nightmares, weight gain
+Haloperidol|Haldol, Serenace|Constipation, diarrhea, dizziness, drowsiness, dry mouth, headache, loss of appetite, nausea, restlessness, stomach upset, trouble sleeping, rash, hives, itching, difficulty breathing, tightness in the chest, swelling of the mouth, swelling of the face, swelling of the lips, swelling of the tongue, blurred vision, other vision changes, confusion, dark urine, decreased sexual ability, decreased urination, difficulty speaking, difficulty swallowing, drooling, enlarged breasts, excessive sweating, unusual sweating, fainting, fast heartbeat, irregular heartbeat, fever, chills, persistent sore throat, hallucinations, mental changes, mood changes, abnormal thinking, agitation, anxiety, missed menstrual period, other menstrual changes, nipple discharge, prolonged erection, painful erection, rigid muscles, stiff muscles, seizures, severe dissiness, persistent dizziness, headache, vomiting, shuffling walk, uncontrolled muscle movements of the arms, uncontrolled m
 uscle movements of the legs, uncontrolled muscle movements of the tongue, uncontrolled muscle movements of the jaw, uncontrolled muscle movements of the cheeks, tremors, twitching, yellowing of the skin, yellowing of the eyes
+Olanzapine|Zyprexa|fever, stiff muscles, sweating, fast heartbeats, uneven heartbeats, jerky muscle movements you cannot control, sudden numbness, sudden weakness, numbness on one side of the body, weakness on one side of the body, sudden headache, confusion, problems with vision, problems with speech, problems with balance, fever, chills, body aches, flu symptoms, white patches inside your mouth, sores inside your mouth, sores on your lips, increased thirst, frequent urination, excessive hunger, excessive weakness, feeling light-headed, fainting, unusual thoughts, unusual behavior, hallucinations, thoughts about hurting yourself, nausea, stomach pain, low fever, loss of appetite, dark urine, clay-colored stools, jaundice, yellowing of the skin, yellowing of the eyes, dizziness, drowsiness, weakness, constipation, dry mouth, swelling in your hands, swelling in your feet, back pain, weight gain, increased appetite, upset stomach
+Perphenazine|Trilafon|Aching of the limbs, numbness of the limbs, brain swelling, breast milk production, diarrhea, drowsiness, dry mouth, low blood pressure upon standing, nausea, rapid heartbeat, irregular heartbeat, restlessness, salivation, seizures, vomiting
+Quetiapine|Seroquel|fever, stiff muscles, confusion, sweating, fast heartbeats, uneven heartbeats, jerky muscle movements you cannot control, sudden numbness, sudden weakness, sudden numbness on one side of the body, sudden weakness on one side of the body, sudden headache, confusion, problems with vision, problems with speech, problems with balance, fever, chills, body aches, flu symptoms, white patches inside your mouth, sores inside your mouth, sores on your lips, increased thirst, frequent urination, excessive hunger, weakness, feeling like you might pass out, urinating less than usual, not urinating at all, dizziness, drowsiness, weakness, dry mouth, runny nose, sore throat, nausea, vomiting, stomach pain, constipation, blurred vision, headache, breast swelling, breast discharge, missed menstrual periods, weight gain
+Risperidone|Risperdal|fever, stiff muscles, confusion, sweating, fast heartbeats, uneven heartbeats, restless muscle movements in your eyes, restless muscle movements in your tongue, restless muscle movements in your jaw, restless muscle movements in your neck, tremor, uncontrolled shaking, fever, chills, body aches, flu symptoms, white patches inside your mouth, sores inside your mouth, sores on your lips, trouble swallowing, feeling light-headed, fainting, mild restlessness, drowsiness, tremor, sleepiness, dreaming more than usual, blurred vision, dizziness, headache, weight gain, problems with urination, nausea, dry mouth, constipation, decreased sex drive, impotence, difficulty having an orgasm
+Thioridazine|Mellaril|Blurred vision, breast development in men, breast milk secretion, constipation, diarrhea, drowsiness, dry mouth, impotence, nausea, swelling in the arms and legs, edema, tardive dyskinesia, involuntary muscle spasms and twitches in the face and body, vomiting
+Ziprasidone|Geodon|dizziness, feeling light-headed, fainting, fast heartbeat, pounding heartbeat, stiff muscles, confusion, sweating, uneven heartbeats, fever, chills, body aches, flu symptoms, white patches inside your mouth, sores inside your mouth, sores on your lips, tremor, uncontrolled shaking, restless muscle movements in your eyes, restless muscle movements in your tongue, restless muscle movements in your jaw, restless muscle movements in your neck, agitation, hostility, confusion, increased thirst, increased urination, weakness, extreme hunger, penis erection that is painful, penis erection lasts 4 hours or longer, mild skin rash, anxiety, headache, depressed mood, dizziness, drowsiness, muscle pain, muscle twitching, nausea, vomiting, loss of appetite, runny nose, stuffy nose, cough, sore throat, weight gain
+Diazepam|Diastat, Diastat Pediatric, Diazepam Intensol, Valium|Decreased coordination, diarrhea, dizziness, drowsiness, headache, nervousness, stomach pain, stuffy nose, rash, hives, itching, difficulty breathing, tightness in the chest, swelling of the mouth, swelling of the face, swelling of the lips, swelling of the tongue, hallucinations, mental changes, mood changes, muscle spasms, muscle twitching, new seizures, worsened seizures, overexcitement, shortness of breath, sleep disturbances, trouble sleeping, wheezing
+Valproic Acid|Depakene, Stavzor|Constipation, diarrhea, dizziness, drowsiness, headache, increased appetite, decreased appetite, mild hair loss, nausea, sore throat, stomach pain, upset stomach, trouble sleeping, vomiting, weight gain, rash, hives, itching, difficulty breathing, tightness in the chest, swelling of the mouth, swelling of the face, swelling of the lips, swelling of the tongue, abnormal thinking, behavior changes, blurred vision, other vision changes, change in menstrual period, change in the amount of urine produced, chest pain, confusion, dark urine, fast heartbeat, irregular heartbeat, fever, chills, persistent sore throat, general feeling of being unwell, hallucinations, hearing loss, joint pain, joint weakness, muscle pain, muscle weakness, loss of coordination, memory loss, mental changes, mood changes, depression, nervousness, pale stools, red skin, swollen skin, blistered skin, ringing in the ears, severe nausea, persistent nausea, vomiting, loss of appetite, s
 evere stomach pain, persistent stomach pain, cramps, sluggishness, suicidal thoughts, suicidal actions, swelling of the arms, swelling of the legs, swollen lymph nodes, tremor, trouble speaking, trouble walking, uncontrolled muscle movements, unusual bleeding, unusual bruising, unusual tiredness, unusual weakness, yellowing of the skin, yellowing of the eyes
+Topiramate|Topamax|sudden vision loss, pain around eyes, pain behind your eyes, dry mouth, increased thirst, confusion, drowsiness, decreased sweating, increased body temperature, hot dry skin, nausea, vomiting, increased urination, muscle pain, muscle weakness, fast heart rate, feeling light-headed, fainting, seizure, convulsions, severe pain in your side, severe pain in your lower back, painful urination, difficult urination, slowed thinking, memory problems, trouble concentrating, problems with speech, problems with balance, numbness, tingling, sleep problems, insomnia, tired feeling, headache, dizziness, loss of appetite, weight loss
+Carbamazepine|Tegretol, Carbatrol, Epitol, Equetro|fever, sore throat, headache with a severe blistering skin, peeling skin, red skin rash, pale skin, easy bruising, easy bleeding, unusual weakness, white patches inside your mouth, sores inside your mouth, sores on your lips, feeling short of breath, swelling of your ankles, swelling of your feet, nausea, stomach pain, loss of appetite, jaundice, yellowing of the skin, yellowing of the eyes, urinating less than usual, feeling dizzy, drowsy, unsteady, vomiting, diarrhea, constipation, stomach pain, confusion, headache, blurred vision, ringing in your ears, dry mouth, swollen tongue, joint pain, muscle pain, leg cramps
+Lamotrigine|Lamictal|the first sign of any skin rash, fever, sore throat, headache with a severe blistering skin, headache with peeling skin, headache with red skin rash, chest pain, pale skin, easy bruising, easy bleeding, fever, chills, body aches, flu symptoms, muscle pain, tenderness, weakness with fever, weakness with flu symptoms and dark colored urine, nausea, stomach pain, low fever, loss of appetite, dark urine, clay-colored stools, jaundice, yellowing of the skin, yellowing of the eyes, dizziness, drowsiness, blurred vision, mild nausea, vomiting, diarrhea, upset stomach, headache, lack of coordination, weight loss, sleep problems, insomnia, unusual dreams, runny nose, stuffy nose
+Gabapentin|Neurontin|increased seizures, fever, chills, body aches, flu symptoms, swelling of your ankles, swelling fo your feet, confusion, rapid back and forth movement of your eyes, tremor, easy bruising, changes in behavior, memory problems, trouble concentrating, acting restless, acting hostile, acting aggressive, dizziness, drowsiness, weakness, tired feeling, lack of coordination, blurred vision, nausea, vomiting, stomach pain, loss of appetite, diarrhea, constipation, dry mouth, runny nose, stuffy nose, sore throat, headache, sleep problems, insomnia, unusual dreams, acne, mild skin rash
+Oxcarbazepine|Trileptal|sore throat, headache with a severe blistering, headache with peeling skin, headache with red skin rash, jaundice, yellowing of the skin, yellowing of the eyes, fever, swollen glands, flu-like symptoms, easy bruising, easy bleeding, unusual weakness, urinating less than usual, not urinating at all, increased seizures, mild nausea, vomiting, stomach pain, diarrhea, problems with speech, problems with balance, problems with coordination, blurred vision, mental slowness, trouble concentrating, tremors, shaking, dizziness, drowsiness, skin rash
+Lithium carbonate|Eskalith, Lithobid|Mild hand tremor, mild thirst, temporary nausea, mild nausea, general discomfort at the beginning of treatment, rash, hives, itching, difficulty breathing, tightness in the chest, swelling of the mouth, swelling of the face, swelling of the lips, swelling of the tongue, blurred vision, confusion, diarrhea, drowsiness, excessive weight gain, fainting, giddiness, inability to control the bladder, inability to control bowels, increased thirst, increased urination, decreased urination, involuntary twitching, involuntary muscle movements, loss of consciousness, loss of coordination, muscle weakness, persistent headache, persistent nausea, severe nausea, ringing in the ears, seizures, slow heartbeat, irregular heartbeat, slurred speech, swelling of the ankles, swelling of the wrists, unsteadiness, vision changes, vomiting
+Amphetamine|Adderall|Adderall XR|fast heartbeats, pounding heartbeats, uneven heartbeats, feeling light-headed, fainting, increased blood pressure, severe headache, blurred vision, trouble concentrating, chest pain, numbness, seizure, tremor, restlessness, hallucinations, unusual behavior, motor tics, muscle twitches, headache, dizziness, sleep problems, insomnia, dry mouth, an unpleasant taste in your mouth, diarrhea, constipation, loss of appetite, weight loss, loss of interest in sex, impotence, difficulty having an orgasm
+Caffeine|No Doz Max. Strength, Revive, Stay Awake, Vivarin, Enerjets, Lucidex|Dizziness, irritability, nausea, nervousness, rash, hives, itching, difficulty breathing, tightness in the chest, swelling of the mouth, swelling of the face, swelling of the lips, swelling of the tongue, diarrhea, shakiness, trouble sleeping, vomiting
+Methylphenidate|Daytrana|fast heartbeats, pounding heartbeats, uneven heartbeats, feeling light-headed, fainting, increased blood pressure, severe headache, blurred vision, trouble concentrating, chest pain, numbness, seizure, redness, swelling, itching, blistering where the skin patch was worn, blistering may also spread areas other than where patch is placed, headache with fever, weakness, joint pain, diarrhea, vomiting, aggression, restlessness, hallucinations, unusual behavior, motor tics, muscle twitches, confusion, crying, feeling irritable, vision problems, mild skin redness, mild skin bumps, itching, nausea, loss of appetite, weight loss, sleep problems, insomnia, stuffy nose, sore throat
+Modafinil|Provigil|fever, sore throat, headache, vomiting with a severe blistering, peeling, and red skin rash, bruising, severe tingling, numbness, pain, muscle weakness, easy bruising, easy bleeding, white patches inside your mouth, sores inside your mouth, sores on your lips, hallucinations, unusual thoughts, unusual behavior, anxiety, chest pain, uneven heart beats, headache, dizziness, feeling nervous, feeling agitated, nausea, diarrhea, trouble sleeping, insomnia, dry mouth
\ No newline at end of file

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Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/types/TypeSystem.xml?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/types/TypeSystem.xml (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/sideeffect/types/TypeSystem.xml Fri Apr 18 19:47:21 2014
@@ -0,0 +1,80 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <name>org.apache.ctakes.sideefect.types.TypeSystem</name>
+  <description/>
+  <version>1.0</version>
+  <imports>
+    <import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
+  </imports>
+  <types>
+    <typeDescription>
+      <name>org.apache.ctakes.sideeffect.type.SideEffectAnnotation</name>
+      <description/>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>sideEffect</name>
+          <description>side effect mention in NamedEntity</description>
+          <rangeTypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>drug</name>
+          <description/>
+          <rangeTypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>sentence</name>
+          <description>sentence containing side effect</description>
+          <rangeTypeName>org.apache.ctakes.sideeffect.type.SESentence</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.sideeffect.type.PSESentence</name>
+      <description>sentence(s) that contains potential side effect and causing drug</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.sideeffect.type.PSESentenceFeature</name>
+      <description/>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>pseSen</name>
+          <description/>
+          <rangeTypeName>org.apache.ctakes.sideeffect.type.PSESentence</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>features</name>
+          <description/>
+          <rangeTypeName>uima.cas.StringArray</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.sideeffect.type.SESentence</name>
+      <description/>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+    </typeDescription>
+  </types>
+</typeSystemDescription>

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Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ArtificialSentenceAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ArtificialSentenceAnnotator.xml?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ArtificialSentenceAnnotator.xml (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ArtificialSentenceAnnotator.xml Fri Apr 18 19:47:21 2014
@@ -0,0 +1,94 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+<primitive>true</primitive>
+<annotatorImplementationName>org.apache.ctakes.core.ae.CopyAnnotator</annotatorImplementationName>
+<analysisEngineMetaData>
+<name>ArtificialSentenceAnnotator</name>
+<description>Artificially creates a new SentenceAnnotation object by treating the entire document as a sentence.  The offset values from the DocumentAnnotation object are transferred over to the new SentenceAnnotation object.</description>
+<version></version>
+<vendor>Mayo</vendor>
+<configurationParameters>
+<configurationParameter>
+<name>srcObjClass</name>
+<description>Source JCas object class.  This must be an object that already exists in the JCas.</description>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+<configurationParameter>
+<name>destObjClass</name>
+<description>Destination JCas object class.  A new JCas object will be created.</description>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+<configurationParameter>
+<name>dataBindMap</name>
+<description>Binds data from source to destination.  Format for each entry is the getter method name of the source to the setter method name of the destination.  e.g. getMyValue|setMyValue</description>
+<type>String</type>
+<multiValued>true</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+</configurationParameters>
+<configurationParameterSettings>
+<nameValuePair>
+<name>srcObjClass</name>
+<value>
+<string>org.apache.uima.jcas.tcas.DocumentAnnotation</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>destObjClass</name>
+<value>
+<string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>dataBindMap</name>
+<value>
+<array>
+<string>getBegin|setBegin</string>
+<string>getEnd|setEnd</string>
+</array>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+<typeSystemDescription/>
+<typePriorities/>
+<fsIndexCollection/>
+<capabilities>
+<capability>
+<inputs/>
+<outputs/>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+<resourceManagerConfiguration/>
+</taeDescription>

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Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/KuRuleBasedClassifierAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/KuRuleBasedClassifierAnnotator.xml?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/KuRuleBasedClassifierAnnotator.xml (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/KuRuleBasedClassifierAnnotator.xml Fri Apr 18 19:47:21 2014
@@ -0,0 +1,86 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <primitive>true</primitive>
+  <annotatorImplementationName>org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator</annotatorImplementationName>
+  <analysisEngineMetaData>
+    <name>KuRuleBasedClassifierAnnotator</name>
+    <description>Known vs Unknow classifier using smoking related keywords</description>
+    <version/>
+    <vendor/>
+    <configurationParameters>
+      <configurationParameter>
+        <name>CaseSensitive</name>
+        <type>Boolean</type>
+        <multiValued>false</multiValued>
+        <mandatory>true</mandatory>
+      </configurationParameter>
+      <configurationParameter>
+        <name>classAttribute</name>
+        <type>String</type>
+        <multiValued>false</multiValued>
+        <mandatory>true</mandatory>
+      </configurationParameter>
+      <configurationParameter>
+        <name>SmokingWordsFile</name>
+        <description>smoking related keywords to identify "known" class</description>
+        <type>String</type>
+        <multiValued>false</multiValued>
+        <mandatory>true</mandatory>
+      </configurationParameter>
+      <configurationParameter>
+        <name>UnknownWordsFile</name>
+        <description>If this word/phrase appears, treat the sentence as UNKNOWN</description>
+        <type>String</type>
+        <multiValued>false</multiValued>
+        <mandatory>true</mandatory>
+      </configurationParameter>
+    </configurationParameters>
+    <configurationParameterSettings>
+      <nameValuePair>
+        <name>SmokingWordsFile</name>
+        <value>
+          <string>org/apache/ctakes/smokingstatus/data/KU/keywords.txt</string>
+        </value>
+      </nameValuePair>
+      <nameValuePair>
+        <name>classAttribute</name>
+        <value>
+          <string>smoking_status</string>
+        </value>
+      </nameValuePair>
+      <nameValuePair>
+        <name>CaseSensitive</name>
+        <value>
+          <boolean>false</boolean>
+        </value>
+      </nameValuePair>
+      <nameValuePair>
+        <name>UnknownWordsFile</name>
+        <value>
+          <string>org/apache/ctakes/smokingstatus/data/KU/unknown_words.txt</string>
+        </value>
+      </nameValuePair>
+    </configurationParameterSettings>
+    <typeSystemDescription>
+      <imports>
+        <import name="org.apache.ctakes.smokingstatus.types.TypeSystem"/>
+      </imports>
+    </typeSystemDescription>
+    <typePriorities/>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <resourceManagerConfiguration/>
+</taeDescription>

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Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/PcsClassifierAnnotator_libsvm.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/PcsClassifierAnnotator_libsvm.xml?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/PcsClassifierAnnotator_libsvm.xml (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/PcsClassifierAnnotator_libsvm.xml Fri Apr 18 19:47:21 2014
@@ -0,0 +1,136 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+<primitive>true</primitive>
+<annotatorImplementationName>org.apache.ctakes.smokingstatus.ae.PcsClassifierAnnotator_libsvm</annotatorImplementationName>
+<analysisEngineMetaData>
+<name>PcsClassifierAnnotator_libsvm</name>
+<description>PCS classifier using libsvm. This annotator plays the same role as PcsBOWFeatureAnnotator.xml, PcsClassifierAnnotator.xml, and BOWFeatureRemovalAnnotator.xml, which use Weka.</description>
+<version></version>
+<vendor></vendor>
+<configurationParameters>
+<configurationParameter>
+<name>CaseSensitive</name>
+<type>Boolean</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+</configurationParameters>
+<configurationParameterSettings>
+<nameValuePair>
+<name>CaseSensitive</name>
+<value>
+<boolean>false</boolean>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+<typeSystemDescription>
+<imports>
+        <import name="org.apache.ctakes.smokingstatus.types.TypeSystem"/>
+</imports>
+</typeSystemDescription>
+<typePriorities/>
+<fsIndexCollection/>
+<capabilities>
+<capability>
+<inputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+</inputs>
+<outputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.smokingstatus.type.libsvms.StringAttributeValue</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.smokingstatus.type.libsvms.NumericAttributeValue</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.smokingstatus.type.libsvms.DateAttributeValue</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.smokingstatus.type.libsvms.AttributeValue</type>
+</outputs>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+<externalResourceDependencies>
+<externalResourceDependency>
+<key>PathOfModel</key>
+<description></description>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
+<optional>false</optional>
+</externalResourceDependency>
+<externalResourceDependency>
+<key>StopWordsFile</key>
+<description></description>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
+<optional>false</optional>
+</externalResourceDependency>
+<externalResourceDependency>
+<key>PCSKeyWordFile</key>
+<description/>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
+<optional>false</optional>
+</externalResourceDependency>
+</externalResourceDependencies>
+<resourceManagerConfiguration>
+<externalResources>
+<externalResource>
+<name>PathOfModelResc</name>
+<description></description>
+<fileResourceSpecifier>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/PCS/pcs_libsvm-2.91.model</fileUrl>
+</fileResourceSpecifier>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
+</externalResource>
+<externalResource>
+<name>PCSKeyWordFileResc</name>
+<description/>
+<fileResourceSpecifier>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/PCS/keywords_PCS.txt</fileUrl>
+</fileResourceSpecifier>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
+</externalResource>
+<externalResource>
+<name>StopWordsFileResc</name>
+<description></description>
+<fileResourceSpecifier>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/PCS/stopwords_PCS.txt</fileUrl>
+</fileResourceSpecifier>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
+</externalResource>
+</externalResources>
+<externalResourceBindings>
+<externalResourceBinding>
+<key>PathOfModel</key>
+<resourceName>PathOfModelResc</resourceName>
+</externalResourceBinding>
+<externalResourceBinding>
+<key>StopWordsFile</key>
+<resourceName>StopWordsFileResc</resourceName>
+</externalResourceBinding>
+<externalResourceBinding>
+<key>PCSKeyWordFile</key>
+<resourceName>PCSKeyWordFileResc</resourceName>
+</externalResourceBinding>
+</externalResourceBindings>
+</resourceManagerConfiguration>
+</taeDescription>

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/PcsClassifierAnnotator_libsvm.xml
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Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml Fri Apr 18 19:47:21 2014
@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <primitive>false</primitive>
+  <delegateAnalysisEngineSpecifiers>
+    <delegateAnalysisEngine key="TokenizerAnnotator">
+      <import name="org.apache.ctakes.core.analysis_engine.TokenizerAnnotator"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="KuRuleBasedClassifierAnnotator">
+      <import location="KuRuleBasedClassifierAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="SentenceDetectAnnotator">
+      <import name="org.apache.ctakes.core.analysis_engine.SentenceDetectorAnnotator"/>
+    </delegateAnalysisEngine>
+  </delegateAnalysisEngineSpecifiers>
+  <analysisEngineMetaData>
+    <name>ProductionPostSentenceAggregate_step1</name>
+    <description>Aggregate TAE used to run the Smoking Status pipeline.  This should be followed by the RecordResolutionCasConsumer.</description>
+    <version/>
+    <vendor/>
+    <configurationParameters searchStrategy="language_fallback"/>
+    <configurationParameterSettings/>
+    <flowConstraints>
+      <fixedFlow>
+        <node>SentenceDetectAnnotator</node>
+        <node>TokenizerAnnotator</node>
+        <node>KuRuleBasedClassifierAnnotator</node>
+      </fixedFlow>
+    </flowConstraints>
+    <typePriorities/>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <resourceManagerConfiguration/>
+</taeDescription>

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml
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Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml Fri Apr 18 19:47:21 2014
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="UTF-8"?><taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <primitive>false</primitive>
+  <delegateAnalysisEngineSpecifiers>
+    <delegateAnalysisEngine key="NegationAnnotator">
+      <import name="org.apache.ctakes.necontexts.desc.NegationAnnotator"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="SentenceAdjuster">
+      <import location="SentenceAdjuster.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="SmokingStatusDictionaryLookupAnnotator">
+      <import location="SmokingStatusDictionaryLookupAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="PcsClassifierAnnotator_libsvm">
+      <import location="PcsClassifierAnnotator_libsvm.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="ArtificialSentenceAnnotator">
+      <import location="ArtificialSentenceAnnotator.xml"/>
+    </delegateAnalysisEngine>
+  </delegateAnalysisEngineSpecifiers>
+  <analysisEngineMetaData>
+    <name>Smoking Status AE</name>
+    <description>Aggregate AE used to run the Smoking Status pipeline.  This should be followed by the RecordResolutionCasConsumer.</description>
+    <version/>
+    <vendor/>
+    <configurationParameters searchStrategy="language_fallback"/>
+    <configurationParameterSettings/>
+    <flowConstraints>
+      <fixedFlow>
+        <node>PcsClassifierAnnotator_libsvm</node>
+        <node>ArtificialSentenceAnnotator</node>
+        <node>SentenceAdjuster</node>
+        <node>SmokingStatusDictionaryLookupAnnotator</node>
+        <node>NegationAnnotator</node>
+      </fixedFlow>
+    </flowConstraints>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <resourceManagerConfiguration/>
+</taeDescription>

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml
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