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From chen...@apache.org
Subject svn commit: r1588552 [2/42] - 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/java/org/apache/ctakes/web/client/servlet/Pipeline.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/java/org/apache/ctakes/web/client/servlet/Pipeline.java?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/java/org/apache/ctakes/web/client/servlet/Pipeline.java (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/java/org/apache/ctakes/web/client/servlet/Pipeline.java Fri Apr 18 19:47:21 2014
@@ -0,0 +1,201 @@
+/**
+ * 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.
+ */
+package org.apache.ctakes.web.client.servlet;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.chunker.ae.Chunker;
+import org.apache.ctakes.chunker.ae.DefaultChunkCreator;
+import org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster;
+import org.apache.ctakes.constituency.parser.ae.ConstituencyParser;
+import org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator;
+import org.apache.ctakes.core.ae.SentenceDetector;
+import org.apache.ctakes.core.ae.SimpleSegmentAnnotator;
+import org.apache.ctakes.core.ae.TokenizerAnnotatorPTB;
+import org.apache.ctakes.core.resource.FileLocator;
+import org.apache.ctakes.core.resource.FileResourceImpl;
+import org.apache.ctakes.core.resource.JdbcConnectionResourceImpl;
+import org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl;
+import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
+import org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE;
+import org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator;
+import org.apache.ctakes.drugner.ae.DrugMentionAnnotator;
+import org.apache.ctakes.postagger.POSTagger;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.Chunk;
+import org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.factory.AggregateBuilder;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.factory.ExternalResourceFactory;
+import org.uimafit.factory.TypePrioritiesFactory;
+import org.uimafit.factory.TypeSystemDescriptionFactory;
+import org.uimafit.util.JCasUtil;
+public class Pipeline {
+
+	public static AggregateBuilder getAggregateBuilder()
+	      throws Exception {
+	    	  AggregateBuilder aggregateBuilder = new AggregateBuilder();
+	    	    
+	    	    // identify segments; use simple segment annotator on non-mayo notes
+	    	    // aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(SimpleSegmentAnnotator.class));
+	    	    
+	    	    // identify sentences
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+	    	            SentenceDetector.class,
+	    	            SentenceDetector.SD_MODEL_FILE_PARAM,
+	    	            "org/apache/ctakes/core/sentdetect/sd-med-model.zip"));
+	    	    // identify tokens
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(TokenizerAnnotatorPTB.class));
+	    	    // merge some tokens
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ContextDependentTokenizerAnnotator.class));
+
+	    	    // identify part-of-speech tags
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+	    	        POSTagger.class,
+	    	        TypeSystemDescriptionFactory.createTypeSystemDescription(),
+	    	        TypePrioritiesFactory.createTypePriorities(Segment.class, Sentence.class, BaseToken.class),
+	    	        POSTagger.POS_MODEL_FILE_PARAM,
+	    	        "org/apache/ctakes/postagger/models/mayo-pos.zip"));
+
+	    	    // identify chunks
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+	    	        Chunker.class,
+	    	        Chunker.CHUNKER_MODEL_FILE_PARAM,
+	    	        "org/apache/ctakes/chunker/models/chunker-model.zip",
+	    	        Chunker.CHUNKER_CREATOR_CLASS_PARAM,
+	    	        DefaultChunkCreator.class));
+
+	    	    // identify UMLS named entities
+
+	    	    // adjust NP in NP NP to span both
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+	    	        ChunkAdjuster.class,
+	    	        ChunkAdjuster.PARAM_CHUNK_PATTERN,
+	    	        new String[] { "NP", "NP" },
+	    	        ChunkAdjuster.PARAM_EXTEND_TO_INCLUDE_TOKEN,
+	    	        1));
+	    	    // adjust NP in NP PP NP to span all three
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+	    	        ChunkAdjuster.class,
+	    	        ChunkAdjuster.PARAM_CHUNK_PATTERN,
+	    	        new String[] { "NP", "PP", "NP" },
+	    	        ChunkAdjuster.PARAM_EXTEND_TO_INCLUDE_TOKEN,
+	    	        2));
+	    	    // add lookup windows for each NP
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
+	    	    // maximize lookup windows
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
+	    	    // add UMLS on top of lookup windows
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+	    	        DictionaryLookupAnnotator.class,
+	    	        "ctakes.umlsaddr",
+	    	        "https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser",
+	    	        "ctakes.umlsvendor",
+	    	        "NLM-6515182895",
+	    	        "LookupDescriptor",
+	    	        ExternalResourceFactory.createExternalResourceDescription(
+	    	            FileResourceImpl.class,
+	    	            FileLocator.locateFile("org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml")),
+	    	        "DbConnection",
+	    	        ExternalResourceFactory.createExternalResourceDescription(
+	    	            JdbcConnectionResourceImpl.class,
+	    	            "",
+	    	            JdbcConnectionResourceImpl.PARAM_DRIVER_CLASS,
+	    	            "org.hsqldb.jdbcDriver",
+	    	            JdbcConnectionResourceImpl.PARAM_URL,
+	    	            // Should be the following but it's WAY too slow
+	    	            // "jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/umls"),
+	    	            "jdbc:hsqldb:res:org/apache/ctakes/dictionary/lookup/umls2011ab/umls"),
+	    	        "RxnormIndexReader",
+	    	        ExternalResourceFactory.createExternalResourceDescription(
+	    	            LuceneIndexReaderResourceImpl.class,
+	    	            "",
+	    	            "UseMemoryIndex",
+	    	            true,
+	    	            "IndexDirectory",
+	    	            FileLocator.locateFile("org/apache/ctakes/dictionary/lookup/rxnorm_index")),
+	    	        "OrangeBookIndexReader",
+	    	        ExternalResourceFactory.createExternalResourceDescription(
+	    	            LuceneIndexReaderResourceImpl.class,
+	    	            "",
+	    	            "UseMemoryIndex",
+	    	            true,
+	    	            "IndexDirectory",
+	    	            FileLocator.locateFile("org/apache/ctakes/dictionary/lookup/OrangeBook"))));
+
+	    	    // add drug signatures
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(DrugMentionAnnotator.class,
+	    	    		DrugMentionAnnotator.PARAM_SEGMENTS_MEDICATION_RELATED,
+	    	    		new String[] { "SIMPLE_SEGMENT" },
+	    	    		DrugMentionAnnotator.DISTANCE,
+	    	    		"1",
+	    	    		DrugMentionAnnotator.BOUNDARY_ANN_TYPE,
+	    	    		"org.apache.ctakes.typesystem.type.textspan.Sentence"));
+
+	    	    // add dependency parser
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ClearNLPDependencyParserAE.class));
+
+	    	    // add semantic role labeler
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ClearNLPSemanticRoleLabelerAE.class));
+
+	    	    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ConstituencyParser.class));
+	    	    
+	    	    return aggregateBuilder;
+	      }
+	
+	  public static class CopyNPChunksToLookupWindowAnnotations extends JCasAnnotator_ImplBase {
+
+		    @Override
+		    public void process(JCas jCas) throws AnalysisEngineProcessException {
+		      for (Chunk chunk : JCasUtil.select(jCas, Chunk.class)) {
+		        if (chunk.getChunkType().equals("NP")) {
+		          new LookupWindowAnnotation(jCas, chunk.getBegin(), chunk.getEnd()).addToIndexes();
+		        }
+		      }
+		    }
+		  }
+		  
+		  public static class RemoveEnclosedLookupWindows extends JCasAnnotator_ImplBase {
+
+		    @Override
+		    public void process(JCas jCas) throws AnalysisEngineProcessException {
+		      List<LookupWindowAnnotation> lws = new ArrayList<LookupWindowAnnotation>(JCasUtil.select(jCas, LookupWindowAnnotation.class));
+		      // we'll navigate backwards so that as we delete things we shorten the list from the back
+		      for(int i = lws.size()-2; i >= 0; i--){
+		        LookupWindowAnnotation lw1 = lws.get(i);
+		        LookupWindowAnnotation lw2 = lws.get(i+1);
+		        if(lw1.getBegin() <= lw2.getBegin() && lw1.getEnd() >= lw2.getEnd()){
+		          /// lw1 envelops or encloses lw2
+		          lws.remove(i+1);
+		          lw2.removeFromIndexes();
+		        }
+		      }
+		      
+		    }
+		    
+		  }
+
+}

Propchange: ctakes/sandbox/ctakes-web-client/src/main/java/org/apache/ctakes/web/client/servlet/Pipeline.java
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    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/META-INF/org.uimafit/types.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/META-INF/org.uimafit/types.txt?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/META-INF/org.uimafit/types.txt (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/META-INF/org.uimafit/types.txt Fri Apr 18 19:47:21 2014
@@ -0,0 +1 @@
+classpath*:org/apache/ctakes/assertion/zoner/types/TypeSystem.xml

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/META-INF/org.uimafit/types.txt
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/all_cues.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/all_cues.txt?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/all_cues.txt (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/all_cues.txt Fri Apr 18 19:47:21 2014
@@ -0,0 +1,454 @@
+conditional	on exertion
+conditional	on exercise
+conditional	with exertion
+conditional	with exercise
+conditional	exertional
+conditional	intolerance
+conditional	after
+conditional	post
+conditional	while
+conditional	when
+conditional	planned
+conditional	in the event
+conditional	if
+conditional	awaiting
+conditional	continued
+conditional	proceed
+conditional	plan
+conditionalavoid	scheduled
+hypothetical	avoiding
+hypothetical	avoidance
+hypothetical	if
+hypothetical	unless
+hypothetical	monitor for
+hypothetical	monitors for
+hypothetical	monitored for
+hypothetical	monitoring for
+hypothetical	prn
+hypothetical	PRN
+hypothetical	p.r.n.
+hypothetical	P.R.N.
+hypothetical	as needed for
+hypothetical	as necessary for 
+hypothetical	call for
+hypothetical	call with
+hypothetical	return for
+hypothetical	return with
+hypothetical	return
+hypothetical	watch for
+hypothetical	report new
+hypothetical	potential
+hypothetical	potentially
+hypothetical	instructions for
+hypothetical	prevent
+hypothetical	preventing
+hypothetical	prevention
+hypothetical	risk
+hypothetical	risk stratification for
+hypothetical	future
+hypothetical	immunization against
+hypothetical	should
+hypothetical	should he experience
+hypothetical	should she experience
+hypothetical	should the patient experience
+hypothetical	prophylaxis
+hypothetical	prophylactic
+negation	not
+negation	n't
+negation	&apos;t
+negation	didn't
+negation	doesn't
+negation	don't
+negation	isn't
+negation	aren't
+negation	wasn't
+negation	weren't
+negation	hadn't
+negation	hasn't
+negation	haven't
+negation	won't
+negation	wouldn't
+negation	never
+negation	no longer
+negation	in no way
+negation	neither
+negation	nor
+negation	none
+negation	nobody
+negation	no one
+negation	nowhere
+negation	no place
+negation	no
+negation	without
+negation	absence of
+negation	free of
+negation	clear of
+negation	clear to
+negation	negative for
+negation	neg for
+negation	negative for
+negation	unremarkable for
+negation	unassociated with
+negation	( - )
+negation	non
+negation	lack of
+negation	lack
+negation	lacked
+negation	lacks
+negation	lacking
+negation	impossible
+negation	cannot
+negation	can't
+negation	couldn't
+negation	inability
+negation	unable
+negation	forget
+negation	forgets
+negation	forgetting
+negation	forgot
+negation	forgotten
+negation	fail
+negation	failed
+negation	failing
+negation	fails
+negation	failure
+negation	free of
+negation	free
+negation	absent
+negation	immune to
+negation	denied
+negation	denies
+negation	deny
+negation	denying
+negation	avoided
+negation	avoids
+negation	prevented
+negation	prevents
+negation	prophylaxis against
+negation	shouldn't
+negation	mustn't
+negation	unwilling
+negation	unwillingness
+negation	reluctance
+negation	reluctant
+negation	decline
+negation	declined
+negation	declines
+negation	declining
+negation	refusal
+negation	refuse
+negation	refused
+negation	refuses
+negation	refusing
+negation	excluded
+negation	excludes
+negation	ruled out
+negation	rules out
+negation	discontinuance
+negation	discontinuation
+negation	discontinue
+negation	discontinued
+negation	discontinues
+negation	discontinuing
+negation	quit
+negation	quits
+negation	quitting
+negation	stop
+negation	stopped
+negation	stopping
+negation	stops
+negation	used to
+negation	held
+negation	hold
+negation	holding
+negation	holds
+negation	on hold
+negation	off
+negation	elimination
+negation	eliminate
+negation	eliminated
+negation	eliminates
+negation	eliminating
+negation	eradication
+negation	eradicate
+negation	eradicated
+negation	eradicates
+negation	eradicating
+negation	removal
+negation	remove
+negation	removed
+negation	removes
+negation	removing
+negation	purge
+negation	purged
+negation	purges
+negation	purging
+negation	wipe out
+negation	wiped out
+negation	wipes out
+negation	wiping out
+negation	rid
+negation	interrupt
+negation	interruption
+negation	interruptions
+negation	resolved
+negation	resolution
+negation	disappeared
+negation	disappearance
+negation	rather than
+negation	instead of
+negation	except
+negation	exception
+negation	besides
+negation	aside from
+negation	other than
+not_patient	mother
+not_patient	father
+not_patient	parent
+not_patient	parents
+not_patient	sister
+not_patient	sisters
+not_patient	brother
+not_patient	brothers
+not_patient	sibling
+not_patient	siblings
+not_patient	grandfather
+not_patient	grandfathers
+not_patient	grandmother
+not_patient	grandmothers
+not_patient	cousin
+not_patient	cousins
+not_patient	aunt
+not_patient	aunts
+not_patient	uncle
+not_patient	uncles
+not_patient	stepfather
+not_patient	stepmother
+not_patient	cousin
+not_patient	cousins
+not_patient	niece
+not_patient	nieces
+not_patient	nephew
+not_patient	nephews
+not_patient	wife
+not_patient	husband
+not_patient	spouse
+not_patient	partner
+not_patient	partners
+not_patient	roommate
+not_patient	roommates
+not_patient	classmate
+not_patient	classmates
+not_patient	friend
+not_patient	friends
+not_patient	acquaintance
+not_patient	acquaintances
+not_patient	individual
+not_patient	individuals
+not_patient	person
+not_patient	persons
+not_patient	relative
+not_patient	relatives
+not_patient	family
+not_patient	family member
+not_patient	family members
+not_patient	familiy history of 
+not_patient	fhx of
+not_patient	fam hx of
+not_patient	family hx
+not_patient	twin
+not_patient	familial
+speculation	uncertain
+speculation	unsure
+speculation	improbable
+speculation	unlikely
+speculation	doubtful
+speculation	doubt
+speculation	doubted
+speculation	doubting
+speculation	doubts
+speculation	possible
+speculation	poss
+speculation	hypothetical
+speculation	questionable
+speculation	consistent with
+speculation	compatible with
+speculation	equivocal for
+speculation	suspicious for
+speculation	potential
+speculation	concerned for
+speculation	concerning for
+speculation	worrisome for
+speculation	unclear
+speculation	unknown
+speculation	possibly
+speculation	potentially
+speculation	maybe
+speculation	perhaps
+speculation	possibilities
+speculation	possibility
+speculation	evidence for
+speculation	evidence of
+speculation	speculation
+speculation	consideration
+speculation	?
+speculation	ddx
+speculation	differential diagnosis
+speculation	differential diagnoses
+speculation	believe
+speculation	believed
+speculation	believes
+speculation	believing
+speculation	consider
+speculation	considered
+speculation	considering
+speculation	considers
+speculation	t/c
+speculation	entertain
+speculation	entertained
+speculation	entertaining
+speculation	entertains
+speculation	question
+speculation	questioned
+speculation	questioning
+speculation	questions
+speculation	speculate
+speculation	speculated
+speculation	speculates
+speculation	speculating
+speculation	can
+speculation	could
+speculation	may
+speculation	might
+speculation	whether or not
+speculation	whether
+speculation	either
+speculation	or
+speculation	if
+speculation	unless
+	probable	prob_adj
+speculation	likely
+speculation	presumed
+speculation	presumptive
+speculation	apparent
+speculation	preliminary
+speculation	putative
+speculation	indicative of
+speculation	suggestive of
+speculation	typical of
+speculation	probably
+speculation	likely
+speculation	presumably
+speculation	apparently
+speculation	reportedly
+speculation	seemingly
+speculation	supposedly
+speculation	must
+speculation	appear
+speculation	appeared
+speculation	appearing
+speculation	appears
+speculation	seem
+speculation	seemed
+speculation	seems
+speculation	seeming
+speculation	estimate
+speculation	estimated
+speculation	estimates
+speculation	estimating
+speculation	feel that
+speculation	feeling that
+speculation	feels that
+speculation	felt that
+speculation	hypothesize
+speculation	hypothesized
+speculation	hypothesizes
+speculation	hypothesizing
+speculation	implied
+speculation	implies
+speculation	imply
+speculation	implying
+speculation	indicate
+speculation	indicated
+speculation	indicates
+speculation	indicating
+speculation	postulate
+speculation	postulated
+speculation	postulating
+speculation	postulates
+speculation	propose
+speculation	proposed
+speculation	proposes
+speculation	proposing
+speculation	suggest
+speculation	suggested
+speculation	suggesting
+speculation	suggests
+speculation	support
+speculation	supported
+speculation	supporting
+speculation	supports
+speculation	suppose
+speculation	supposed
+speculation	supposes
+speculation	supposing
+speculation	suspect
+speculation	suspected
+speculation	suspecting
+speculation	suspects
+speculation	think
+speculation	thinks
+speculation	thinking
+speculation	thought
+speculation	concern for
+speculation	concerns for
+speculation	implication
+speculation	implications
+speculation	impression of
+speculation	indication of
+speculation	indications of
+speculation	suspicion
+speculation	suspicions
+speculation	suggestion
+speculation	suggestions
+speculation	hypothesis
+speculation	hypotheses
+speculation	probability
+speculation	probabilities
+speculation	sign of
+speculation	signs of
+speculation	v.s.
+speculation	versus
+speculation	vs.
+speculation	vs
+speculation	r / o
+speculation	ro
+speculation	r/o
+speculation	rule out
+speculation	ruling out
+speculation	rule - out
+speculation	ruling - out
+speculation	test for
+speculation	tested for
+speculation	testing for
+speculation	tests for
+speculation	check for
+speculation	checked for
+speculation	checking for
+speculation	checks for
+speculation	evaluate for
+speculation	eval for
+speculation	evaluated for
+speculation	evaluates for
+speculation	evaluating for
+speculation	evaluation for
+speculation	assess for
+speculation	assessment for
+speculation	monitor for
+speculation	monitored for
+speculation	monitoring for
+speculation	monitors for
+speculation	seriologies for
+speculation	seriology for
+speculation	work up for
+speculation	workup for

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/all_cues.txt
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Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words.txt?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words.txt (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words.txt Fri Apr 18 19:47:21 2014
@@ -0,0 +1,454 @@
+on exertion|conditional|conditional
+on exercise|conditional|conditional
+with exertion|conditional|conditional
+with exercise|conditional|conditional
+exertional|conditional|conditional
+intolerance|conditional|conditional
+after|conditional|conditional
+post|conditional|conditional
+while|conditional|conditional
+when|conditional|conditional
+planned|conditional|conditional
+in the event|conditional|conditional
+if|conditional|conditional
+awaiting|conditional|conditional
+continued|conditional|conditional
+proceed|conditional|conditional
+plan|conditional|conditional
+scheduled|conditional|conditionalavoid|hypothetical|hypothetical
+avoiding|hypothetical|hypothetical
+avoidance|hypothetical|hypothetical
+if|hypothetical|hypothetical
+unless|hypothetical|hypothetical
+monitor for|hypothetical|hypothetical
+monitors for|hypothetical|hypothetical
+monitored for|hypothetical|hypothetical
+monitoring for|hypothetical|hypothetical
+prn|hypothetical|hypothetical
+PRN|hypothetical|hypothetical
+p.r.n.|hypothetical|hypothetical
+P.R.N.|hypothetical|hypothetical
+as needed for|hypothetical|hypothetical
+as necessary for |hypothetical|hypothetical
+call for|hypothetical|hypothetical
+call with|hypothetical|hypothetical
+return for|hypothetical|hypothetical
+return with|hypothetical|hypothetical
+return|hypothetical|hypothetical
+watch for|hypothetical|hypothetical
+report new|hypothetical|hypothetical
+potential|hypothetical|hypothetical
+potentially|hypothetical|hypothetical
+instructions for|hypothetical|hypothetical
+prevent|hypothetical|hypothetical
+preventing|hypothetical|hypothetical
+prevention|hypothetical|hypothetical
+risk|hypothetical|hypothetical
+risk stratification for|hypothetical|hypothetical
+future|hypothetical|hypothetical
+immunization against|hypothetical|hypothetical
+should|hypothetical|hypothetical
+should he experience|hypothetical|hypothetical
+should she experience|hypothetical|hypothetical
+should the patient experience|hypothetical|hypothetical
+prophylaxis|hypothetical|hypothetical
+prophylactic|hypothetical|hypothetical
+not|not|negation
+n't|not|negation
+&apos;t|not|negation
+didn't|not|negation
+doesn't|not|negation
+don't|not|negation
+isn't|not|negation
+aren't|not|negation
+wasn't|not|negation
+weren't|not|negation
+hadn't|not|negation
+hasn't|not|negation
+haven't|not|negation
+won't|not|negation
+wouldn't|not|negation
+never|not|negation
+no longer|not|negation
+in no way|not|negation
+neither|neither|negation
+nor|neither|negation
+none|none|negation
+nobody|none|negation
+no one|none|negation
+nowhere|none|negation
+no place|none|negation
+no|no|negation
+without|no|negation
+absence of|no|negation
+free of|no|negation
+clear of|no|negation
+clear to|no|negation
+negative for|no|negation
+neg for|no|negation
+negative for|no|negation
+unremarkable for|no|negation
+unassociated with|no|negation
+( - )|no|negation
+non|no|negation
+lack of|no|negation
+lack|no|negation
+lacked|no|negation
+lacks|no|negation
+lacking|no|negation
+impossible|fail|negation
+cannot|fail|negation
+can't|fail|negation
+couldn't|fail|negation
+inability|fail|negation
+unable|fail|negation
+forget|fail|negation
+forgets|fail|negation
+forgetting|fail|negation
+forgot|fail|negation
+forgotten|fail|negation
+fail|fail|negation
+failed|fail|negation
+failing|fail|negation
+fails|fail|negation
+failure|fail|negation
+free of|absent|negation
+free|absent|negation
+absent|absent|negation
+immune to|absent|negation
+denied|deny|negation
+denies|deny|negation
+deny|deny|negation
+denying|deny|negation
+avoided|avoid|negation
+avoids|avoid|negation
+prevented|avoid|negation
+prevents|avoid|negation
+prophylaxis against|avoid|negation
+shouldn't|avoid|negation
+mustn't|avoid|negation
+unwilling|decline|negation
+unwillingness|decline|negation
+reluctance|decline|negation
+reluctant|decline|negation
+decline|decline|negation
+declined|decline|negation
+declines|decline|negation
+declining|decline|negation
+refusal|decline|negation
+refuse|decline|negation
+refused|decline|negation
+refuses|decline|negation
+refusing|decline|negation
+excluded|ruleout|negation
+excludes|ruleout|negation
+ruled out|ruleout|negation
+rules out|ruleout|negation
+discontinuance|stop|negation
+discontinuation|stop|negation
+discontinue|stop|negation
+discontinued|stop|negation
+discontinues|stop|negation
+discontinuing|stop|negation
+quit|stop|negation
+quits|stop|negation
+quitting|stop|negation
+stop|stop|negation
+stopped|stop|negation
+stopping|stop|negation
+stops|stop|negation
+used to|stop|negation
+held|stop|negation
+hold|stop|negation
+holding|stop|negation
+holds|stop|negation
+on hold|stop|negation
+off|stop|negation
+elimination|stop|negation
+eliminate|stop|negation
+eliminated|stop|negation
+eliminates|stop|negation
+eliminating|stop|negation
+eradication|stop|negation
+eradicate|stop|negation
+eradicated|stop|negation
+eradicates|stop|negation
+eradicating|stop|negation
+removal|stop|negation
+remove|stop|negation
+removed|stop|negation
+removes|stop|negation
+removing|stop|negation
+purge|stop|negation
+purged|stop|negation
+purges|stop|negation
+purging|stop|negation
+wipe out|stop|negation
+wiped out|stop|negation
+wipes out|stop|negation
+wiping out|stop|negation
+rid|stop|negation
+interrupt|stop|negation
+interruption|stop|negation
+interruptions|stop|negation
+resolved|disappear|negation
+resolution|disappear|negation
+disappeared|disappear|negation
+disappearance|disappear|negation
+rather than|exception|negation
+instead of|exception|negation
+except|exception|negation
+exception|exception|negation
+besides|exception|negation
+aside from|exception|negation
+other than|exception|negation
+mother|not_patient|not_patient
+father|not_patient|not_patient
+parent|not_patient|not_patient
+parents|not_patient|not_patient
+sister|not_patient|not_patient
+sisters|not_patient|not_patient
+brother|not_patient|not_patient
+brothers|not_patient|not_patient
+sibling|not_patient|not_patient
+siblings|not_patient|not_patient
+grandfather|not_patient|not_patient
+grandfathers|not_patient|not_patient
+grandmother|not_patient|not_patient
+grandmothers|not_patient|not_patient
+cousin|not_patient|not_patient
+cousins|not_patient|not_patient
+aunt|not_patient|not_patient
+aunts|not_patient|not_patient
+uncle|not_patient|not_patient
+uncles|not_patient|not_patient
+stepfather|not_patient|not_patient
+stepmother|not_patient|not_patient
+cousin|not_patient|not_patient
+cousins|not_patient|not_patient
+niece|not_patient|not_patient
+nieces|not_patient|not_patient
+nephew|not_patient|not_patient
+nephews|not_patient|not_patient
+wife|not_patient|not_patient
+husband|not_patient|not_patient
+spouse|not_patient|not_patient
+partner|not_patient|not_patient
+partners|not_patient|not_patient
+roommate|not_patient|not_patient
+roommates|not_patient|not_patient
+classmate|not_patient|not_patient
+classmates|not_patient|not_patient
+friend|not_patient|not_patient
+friends|not_patient|not_patient
+acquaintance|not_patient|not_patient
+acquaintances|not_patient|not_patient
+individual|not_patient|not_patient
+individuals|not_patient|not_patient
+person|not_patient|not_patient
+persons|not_patient|not_patient
+relative|not_patient|not_patient
+relatives|not_patient|not_patient
+family|not_patient|not_patient
+family member|not_patient|not_patient
+family members|not_patient|not_patient
+familiy history of |not_patient|not_patient
+fhx of|not_patient|not_patient
+fam hx of|not_patient|not_patient
+family hx|not_patient|not_patient
+twin|not_patient|not_patient
+familial|not_patient|not_patient
+uncertain|speculation_mid|speculation
+unsure|speculation_mid|speculation
+improbable|speculation_low|speculation
+unlikely|speculation_low|speculation
+doubtful|speculation_low|speculation
+doubt|speculation_low|speculation
+doubted|speculation_low|speculation
+doubting|speculation_low|speculation
+doubts|speculation_low|speculation
+possible|speculation_mid|speculation
+poss|speculation_mid|speculation
+hypothetical|speculation_mid|speculation
+questionable|speculation_mid|speculation
+consistent with|speculation_mid|speculation
+compatible with|speculation_mid|speculation
+equivocal for|speculation_mid|speculation
+suspicious for|speculation_mid|speculation
+potential|speculation_mid|speculation
+concerned for|speculation_mid|speculation
+concerning for|speculation_mid|speculation
+worrisome for|speculation_mid|speculation
+unclear|speculation_mid|speculation
+unknown|speculation_mid|speculation
+possibly|speculation_mid|speculation
+potentially|speculation_mid|speculation
+maybe|speculation_mid|speculation
+perhaps|speculation_mid|speculation
+possibilities|speculation_mid|speculation
+possibility|speculation_mid|speculation
+evidence for|speculation_mid|speculation
+evidence of|speculation_mid|speculation
+speculation|speculation_mid|speculation
+consideration|speculation_mid|speculation
+?|speculation_mid|speculation
+ddx|speculation_mid|speculation
+differential diagnosis|speculation_mid|speculation
+differential diagnoses|speculation_mid|speculation
+believe|speculation_high|speculation
+believed|speculation_high|speculation
+believes|speculation_high|speculation
+believing|speculation_high|speculation
+consider|speculation_mid|speculation
+considered|speculation_mid|speculation
+considering|speculation_mid|speculation
+considers|speculation_mid|speculation
+t/c|speculation_mid|speculation
+entertain|speculation_mid|speculation
+entertained|speculation_mid|speculation
+entertaining|speculation_mid|speculation
+entertains|speculation_mid|speculation
+question|speculation_mid|speculation
+questioned|speculation_mid|speculation
+questioning|speculation_mid|speculation
+questions|speculation_mid|speculation
+speculate|speculation_high|speculation
+speculated|speculation_high|speculation
+speculates|speculation_high|speculation
+speculating|speculation_high|speculation
+can|speculation_mid|speculation
+could|speculation_mid|speculation
+may|speculation_mid|speculation
+might|speculation_mid|speculation
+whether or not|speculation_mid|speculation
+whether|speculation_mid|speculation
+either|speculation_mid|speculation
+or|speculation_mid|speculation
+if|speculation_mid|speculation
+unless|speculation_low|speculation
+probable	prob_adj
+likely|speculation_high|speculation
+presumed|speculation_high|speculation
+presumptive|speculation_high|speculation
+apparent|speculation_high|speculation
+preliminary|speculation_high|speculation
+putative|speculation_high|speculation
+indicative of|speculation_high|speculation
+suggestive of|speculation_high|speculation
+typical of|speculation_high|speculation
+probably|speculation_high|speculation
+likely|speculation_high|speculation
+presumably|speculation_high|speculation
+apparently|speculation_high|speculation
+reportedly|speculation_high|speculation
+seemingly|speculation_high|speculation
+supposedly|speculation_high|speculation
+must|speculation_high|speculation
+appear|speculation_high|speculation
+appeared|speculation_high|speculation
+appearing|speculation_high|speculation
+appears|speculation_high|speculation
+seem|speculation_high|speculation
+seemed|speculation_high|speculation
+seems|speculation_high|speculation
+seeming|speculation_high|speculation
+estimate|speculation_high|speculation
+estimated|speculation_high|speculation
+estimates|speculation_high|speculation
+estimating|speculation_high|speculation
+feel that|speculation_high|speculation
+feeling that|speculation_high|speculation
+feels that|speculation_high|speculation
+felt that|speculation_high|speculation
+hypothesize|speculation_high|speculation
+hypothesized|speculation_high|speculation
+hypothesizes|speculation_high|speculation
+hypothesizing|speculation_high|speculation
+implied|speculation_high|speculation
+implies|speculation_high|speculation
+imply|speculation_high|speculation
+implying|speculation_high|speculation
+indicate|speculation_high|speculation
+indicated|speculation_high|speculation
+indicates|speculation_high|speculation
+indicating|speculation_high|speculation
+postulate|speculation_high|speculation
+postulated|speculation_high|speculation
+postulating|speculation_high|speculation
+postulates|speculation_high|speculation
+propose|speculation_high|speculation
+proposed|speculation_high|speculation
+proposes|speculation_high|speculation
+proposing|speculation_high|speculation
+suggest|speculation_high|speculation
+suggested|speculation_high|speculation
+suggesting|speculation_high|speculation
+suggests|speculation_high|speculation
+support|speculation_high|speculation
+supported|speculation_high|speculation
+supporting|speculation_high|speculation
+supports|speculation_high|speculation
+suppose|speculation_high|speculation
+supposed|speculation_high|speculation
+supposes|speculation_high|speculation
+supposing|speculation_high|speculation
+suspect|speculation_high|speculation
+suspected|speculation_high|speculation
+suspecting|speculation_high|speculation
+suspects|speculation_high|speculation
+think|speculation_high|speculation
+thinks|speculation_high|speculation
+thinking|speculation_high|speculation
+thought|speculation_high|speculation
+concern for|speculation_high|speculation
+concerns for|speculation_high|speculation
+implication|speculation_high|speculation
+implications|speculation_high|speculation
+impression of|speculation_high|speculation
+indication of|speculation_high|speculation
+indications of|speculation_high|speculation
+suspicion|speculation_high|speculation
+suspicions|speculation_high|speculation
+suggestion|speculation_high|speculation
+suggestions|speculation_high|speculation
+hypothesis|speculation_high|speculation
+hypotheses|speculation_high|speculation
+probability|speculation_high|speculation
+probabilities|speculation_high|speculation
+sign of|speculation_high|speculation
+signs of|speculation_high|speculation
+v.s.|speculation_high|speculation
+versus|speculation_high|speculation
+vs.|speculation_high|speculation
+vs|speculation_high|speculation
+r / o|speculation_mid|speculation
+ro|speculation_mid|speculation
+r/o|speculation_mid|speculation
+rule out|speculation_mid|speculation
+ruling out|speculation_mid|speculation
+rule - out|speculation_mid|speculation
+ruling - out|speculation_mid|speculation
+test for|speculation_mid|speculation
+tested for|speculation_mid|speculation
+testing for|speculation_mid|speculation
+tests for|speculation_mid|speculation
+check for|speculation_mid|speculation
+checked for|speculation_mid|speculation
+checking for|speculation_mid|speculation
+checks for|speculation_mid|speculation
+evaluate for|speculation_mid|speculation
+eval for|speculation_mid|speculation
+evaluated for|speculation_mid|speculation
+evaluates for|speculation_mid|speculation
+evaluating for|speculation_mid|speculation
+evaluation for|speculation_mid|speculation
+assess for|speculation_mid|speculation
+assessment for|speculation_mid|speculation
+monitor for|speculation_mid|speculation
+monitored for|speculation_mid|speculation
+monitoring for|speculation_mid|speculation
+monitors for|speculation_mid|speculation
+seriologies for|speculation_mid|speculation
+seriology for|speculation_mid|speculation
+work up for|speculation_mid|speculation
+workup for|speculation_mid|speculation

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

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/conditional.psv
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/conditional.psv?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/conditional.psv (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/conditional.psv Fri Apr 18 19:47:21 2014
@@ -0,0 +1,13 @@
+on exertion|conditional|conditional
+on exercise|conditional|conditional
+with exertion|conditional|conditional
+with exercise|conditional|conditional
+exertional|conditional|conditional
+allergy|conditional|conditional
+allergies|conditional|conditional
+allergic to|conditional|conditional
+intolerance|conditional|conditional
+after|conditional|conditional
+post|conditional|conditional
+while|conditional|conditional
+when|conditional|conditional

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/hypothetical.psv
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/hypothetical.psv?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/hypothetical.psv (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/hypothetical.psv Fri Apr 18 19:47:21 2014
@@ -0,0 +1,38 @@
+avoid|hypothetical|hypothetical
+avoiding|hypothetical|hypothetical
+avoidance|hypothetical|hypothetical
+if|hypothetical|hypothetical
+unless|hypothetical|hypothetical
+monitor for|hypothetical|hypothetical
+monitors for|hypothetical|hypothetical
+monitored for|hypothetical|hypothetical
+monitoring for|hypothetical|hypothetical
+prn|hypothetical|hypothetical
+PRN|hypothetical|hypothetical
+p.r.n.|hypothetical|hypothetical
+P.R.N.|hypothetical|hypothetical
+as needed for|hypothetical|hypothetical
+as necessary for |hypothetical|hypothetical
+call for|hypothetical|hypothetical
+call with|hypothetical|hypothetical
+return for|hypothetical|hypothetical
+return with|hypothetical|hypothetical
+return|hypothetical|hypothetical
+watch for|hypothetical|hypothetical
+report new|hypothetical|hypothetical
+potential|hypothetical|hypothetical
+potentially|hypothetical|hypothetical
+instructions for|hypothetical|hypothetical
+prevent|hypothetical|hypothetical
+preventing|hypothetical|hypothetical
+prevention|hypothetical|hypothetical
+risk|hypothetical|hypothetical
+risk stratification for|hypothetical|hypothetical
+future|hypothetical|hypothetical
+immunization against|hypothetical|hypothetical
+should|hypothetical|hypothetical
+should he experience|hypothetical|hypothetical
+should she experience|hypothetical|hypothetical
+should the patient experience|hypothetical|hypothetical
+prophylaxis|hypothetical|hypothetical
+prophylactic|hypothetical|hypothetical

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/negation_cue_class.psv
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/negation_cue_class.psv?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/negation_cue_class.psv (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/negation_cue_class.psv Fri Apr 18 19:47:21 2014
@@ -0,0 +1,149 @@
+not|not|negation
+n't|not|negation
+&apos;t|not|negation
+didn't|not|negation
+doesn't|not|negation
+don't|not|negation
+isn't|not|negation
+aren't|not|negation
+wasn't|not|negation
+weren't|not|negation
+hadn't|not|negation
+hasn't|not|negation
+haven't|not|negation
+won't|not|negation
+wouldn't|not|negation
+never|not|negation
+no longer|not|negation
+in no way|not|negation
+neither|neither|negation
+nor|neither|negation
+none|none|negation
+nobody|none|negation
+no one|none|negation
+nowhere|none|negation
+no place|none|negation
+no|no|negation
+without|no|negation
+absence of|no|negation
+free of|no|negation
+clear of|no|negation
+clear to|no|negation
+negative for|no|negation
+neg for|no|negation
+negative for|no|negation
+unremarkable for|no|negation
+unassociated with|no|negation
+( - )|no|negation
+non|no|negation
+lack of|no|negation
+lack|no|negation
+lacked|no|negation
+lacks|no|negation
+lacking|no|negation
+impossible|fail|negation
+cannot|fail|negation
+can't|fail|negation
+couldn't|fail|negation
+inability|fail|negation
+unable|fail|negation
+forget|fail|negation
+forgets|fail|negation
+forgetting|fail|negation
+forgot|fail|negation
+forgotten|fail|negation
+fail|fail|negation
+failed|fail|negation
+failing|fail|negation
+fails|fail|negation
+failure|fail|negation
+free of|absent|negation
+free|absent|negation
+absent|absent|negation
+immune to|absent|negation
+denied|deny|negation
+denies|deny|negation
+deny|deny|negation
+denying|deny|negation
+avoided|avoid|negation
+avoids|avoid|negation
+prevented|avoid|negation
+prevents|avoid|negation
+prophylaxis against|avoid|negation
+shouldn't|avoid|negation
+mustn't|avoid|negation
+unwilling|decline|negation
+unwillingness|decline|negation
+reluctance|decline|negation
+reluctant|decline|negation
+decline|decline|negation
+declined|decline|negation
+declines|decline|negation
+declining|decline|negation
+refusal|decline|negation
+refuse|decline|negation
+refused|decline|negation
+refuses|decline|negation
+refusing|decline|negation
+excluded|ruleout|negation
+excludes|ruleout|negation
+ruled out|ruleout|negation
+rules out|ruleout|negation
+discontinuance|stop|negation
+discontinuation|stop|negation
+discontinue|stop|negation
+discontinued|stop|negation
+discontinues|stop|negation
+discontinuing|stop|negation
+quit|stop|negation
+quits|stop|negation
+quitting|stop|negation
+stop|stop|negation
+stopped|stop|negation
+stopping|stop|negation
+stops|stop|negation
+used to|stop|negation
+held|stop|negation
+hold|stop|negation
+holding|stop|negation
+holds|stop|negation
+on hold|stop|negation
+off|stop|negation
+elimination|stop|negation
+eliminate|stop|negation
+eliminated|stop|negation
+eliminates|stop|negation
+eliminating|stop|negation
+eradication|stop|negation
+eradicate|stop|negation
+eradicated|stop|negation
+eradicates|stop|negation
+eradicating|stop|negation
+removal|stop|negation
+remove|stop|negation
+removed|stop|negation
+removes|stop|negation
+removing|stop|negation
+purge|stop|negation
+purged|stop|negation
+purges|stop|negation
+purging|stop|negation
+wipe out|stop|negation
+wiped out|stop|negation
+wipes out|stop|negation
+wiping out|stop|negation
+rid|stop|negation
+interrupt|stop|negation
+interruption|stop|negation
+interruptions|stop|negation
+resolved|disappear|negation
+resolution|disappear|negation
+disappeared|disappear|negation
+disappearance|disappear|negation
+rather than|exception|negation
+instead of|exception|negation
+except|exception|negation
+exception|exception|negation
+besides|exception|negation
+aside from|exception|negation
+other than|exception|negation

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/not_patient_cue_list.psv
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/not_patient_cue_list.psv?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/not_patient_cue_list.psv (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/not_patient_cue_list.psv Fri Apr 18 19:47:21 2014
@@ -0,0 +1,56 @@
+mother|not_patient|not_patient
+father|not_patient|not_patient
+parent|not_patient|not_patient
+parents|not_patient|not_patient
+sister|not_patient|not_patient
+sisters|not_patient|not_patient
+brother|not_patient|not_patient
+brothers|not_patient|not_patient
+sibling|not_patient|not_patient
+siblings|not_patient|not_patient
+grandfather|not_patient|not_patient
+grandfathers|not_patient|not_patient
+grandmother|not_patient|not_patient
+grandmothers|not_patient|not_patient
+cousin|not_patient|not_patient
+cousins|not_patient|not_patient
+aunt|not_patient|not_patient
+aunts|not_patient|not_patient
+uncle|not_patient|not_patient
+uncles|not_patient|not_patient
+stepfather|not_patient|not_patient
+stepmother|not_patient|not_patient
+cousin|not_patient|not_patient
+cousins|not_patient|not_patient
+niece|not_patient|not_patient
+nieces|not_patient|not_patient
+nephew|not_patient|not_patient
+nephews|not_patient|not_patient
+wife|not_patient|not_patient
+husband|not_patient|not_patient
+spouse|not_patient|not_patient
+partner|not_patient|not_patient
+partners|not_patient|not_patient
+roommate|not_patient|not_patient
+roommates|not_patient|not_patient
+classmate|not_patient|not_patient
+classmates|not_patient|not_patient
+friend|not_patient|not_patient
+friends|not_patient|not_patient
+acquaintance|not_patient|not_patient
+acquaintances|not_patient|not_patient
+individual|not_patient|not_patient
+individuals|not_patient|not_patient
+person|not_patient|not_patient
+persons|not_patient|not_patient
+relative|not_patient|not_patient
+relatives|not_patient|not_patient
+family|not_patient|not_patient
+family member|not_patient|not_patient
+family members|not_patient|not_patient
+familiy history of |not_patient|not_patient
+fhx of|not_patient|not_patient
+fam hx of|not_patient|not_patient
+family hx|not_patient|not_patient
+twin|not_patient|not_patient
+familial|not_patient|not_patient

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/speculation.psv
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/speculation.psv?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/speculation.psv (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/cue_words/speculation.psv Fri Apr 18 19:47:21 2014
@@ -0,0 +1,194 @@
+uncertain|speculation_mid|speculation
+unsure|speculation_mid|speculation
+improbable|speculation_low|speculation
+unlikely|speculation_low|speculation
+doubtful|speculation_low|speculation
+doubt|speculation_low|speculation
+doubted|speculation_low|speculation
+doubting|speculation_low|speculation
+doubts|speculation_low|speculation
+possible|speculation_mid|speculation
+poss|speculation_mid|speculation
+hypothetical|speculation_mid|speculation
+questionable|speculation_mid|speculation
+consistent with|speculation_mid|speculation
+compatible with|speculation_mid|speculation
+equivocal for|speculation_mid|speculation
+suspicious for|speculation_mid|speculation
+potential|speculation_mid|speculation
+concerned for|speculation_mid|speculation
+concerning for|speculation_mid|speculation
+worrisome for|speculation_mid|speculation
+unclear|speculation_mid|speculation
+unknown|speculation_mid|speculation
+possibly|speculation_mid|speculation
+potentially|speculation_mid|speculation
+maybe|speculation_mid|speculation
+perhaps|speculation_mid|speculation
+possibilities|speculation_mid|speculation
+possibility|speculation_mid|speculation
+evidence for|speculation_mid|speculation
+evidence of|speculation_mid|speculation
+speculation|speculation_mid|speculation
+consideration|speculation_mid|speculation
+?|speculation_mid|speculation
+ddx|speculation_mid|speculation
+differential diagnosis|speculation_mid|speculation
+differential diagnoses|speculation_mid|speculation
+believe|speculation_high|speculation
+believed|speculation_high|speculation
+believes|speculation_high|speculation
+believing|speculation_high|speculation
+consider|speculation_mid|speculation
+considered|speculation_mid|speculation
+considering|speculation_mid|speculation
+considers|speculation_mid|speculation
+t/c|speculation_mid|speculation
+entertain|speculation_mid|speculation
+entertained|speculation_mid|speculation
+entertaining|speculation_mid|speculation
+entertains|speculation_mid|speculation
+question|speculation_mid|speculation
+questioned|speculation_mid|speculation
+questioning|speculation_mid|speculation
+questions|speculation_mid|speculation
+speculate|speculation_high|speculation
+speculated|speculation_high|speculation
+speculates|speculation_high|speculation
+speculating|speculation_high|speculation
+can|speculation_mid|speculation
+could|speculation_mid|speculation
+may|speculation_mid|speculation
+might|speculation_mid|speculation
+whether or not|speculation_mid|speculation
+whether|speculation_mid|speculation
+either|speculation_mid|speculation
+or|speculation_mid|speculation
+if|speculation_mid|speculation
+unless|speculation_low|speculation
+probable	prob_adj
+likely|speculation_high|speculation
+presumed|speculation_high|speculation
+presumptive|speculation_high|speculation
+apparent|speculation_high|speculation
+preliminary|speculation_high|speculation
+putative|speculation_high|speculation
+indicative of|speculation_high|speculation
+suggestive of|speculation_high|speculation
+typical of|speculation_high|speculation
+probably|speculation_high|speculation
+likely|speculation_high|speculation
+presumably|speculation_high|speculation
+apparently|speculation_high|speculation
+reportedly|speculation_high|speculation
+seemingly|speculation_high|speculation
+supposedly|speculation_high|speculation
+must|speculation_high|speculation
+appear|speculation_high|speculation
+appeared|speculation_high|speculation
+appearing|speculation_high|speculation
+appears|speculation_high|speculation
+seem|speculation_high|speculation
+seemed|speculation_high|speculation
+seems|speculation_high|speculation
+seeming|speculation_high|speculation
+estimate|speculation_high|speculation
+estimated|speculation_high|speculation
+estimates|speculation_high|speculation
+estimating|speculation_high|speculation
+feel that|speculation_high|speculation
+feeling that|speculation_high|speculation
+feels that|speculation_high|speculation
+felt that|speculation_high|speculation
+hypothesize|speculation_high|speculation
+hypothesized|speculation_high|speculation
+hypothesizes|speculation_high|speculation
+hypothesizing|speculation_high|speculation
+implied|speculation_high|speculation
+implies|speculation_high|speculation
+imply|speculation_high|speculation
+implying|speculation_high|speculation
+indicate|speculation_high|speculation
+indicated|speculation_high|speculation
+indicates|speculation_high|speculation
+indicating|speculation_high|speculation
+postulate|speculation_high|speculation
+postulated|speculation_high|speculation
+postulating|speculation_high|speculation
+postulates|speculation_high|speculation
+propose|speculation_high|speculation
+proposed|speculation_high|speculation
+proposes|speculation_high|speculation
+proposing|speculation_high|speculation
+suggest|speculation_high|speculation
+suggested|speculation_high|speculation
+suggesting|speculation_high|speculation
+suggests|speculation_high|speculation
+support|speculation_high|speculation
+supported|speculation_high|speculation
+supporting|speculation_high|speculation
+supports|speculation_high|speculation
+suppose|speculation_high|speculation
+supposed|speculation_high|speculation
+supposes|speculation_high|speculation
+supposing|speculation_high|speculation
+suspect|speculation_high|speculation
+suspected|speculation_high|speculation
+suspecting|speculation_high|speculation
+suspects|speculation_high|speculation
+think|speculation_high|speculation
+thinks|speculation_high|speculation
+thinking|speculation_high|speculation
+thought|speculation_high|speculation
+concern for|speculation_high|speculation
+concerns for|speculation_high|speculation
+implication|speculation_high|speculation
+implications|speculation_high|speculation
+impression of|speculation_high|speculation
+indication of|speculation_high|speculation
+indications of|speculation_high|speculation
+suspicion|speculation_high|speculation
+suspicions|speculation_high|speculation
+suggestion|speculation_high|speculation
+suggestions|speculation_high|speculation
+hypothesis|speculation_high|speculation
+hypotheses|speculation_high|speculation
+probability|speculation_high|speculation
+probabilities|speculation_high|speculation
+sign of|speculation_high|speculation
+signs of|speculation_high|speculation
+v.s.|speculation_high|speculation
+versus|speculation_high|speculation
+vs.|speculation_high|speculation
+vs|speculation_high|speculation
+r / o|speculation_mid|speculation
+ro|speculation_mid|speculation
+r/o|speculation_mid|speculation
+rule out|speculation_mid|speculation
+ruling out|speculation_mid|speculation
+rule - out|speculation_mid|speculation
+ruling - out|speculation_mid|speculation
+test for|speculation_mid|speculation
+tested for|speculation_mid|speculation
+testing for|speculation_mid|speculation
+tests for|speculation_mid|speculation
+check for|speculation_mid|speculation
+checked for|speculation_mid|speculation
+checking for|speculation_mid|speculation
+checks for|speculation_mid|speculation
+evaluate for|speculation_mid|speculation
+eval for|speculation_mid|speculation
+evaluated for|speculation_mid|speculation
+evaluates for|speculation_mid|speculation
+evaluating for|speculation_mid|speculation
+evaluation for|speculation_mid|speculation
+assess for|speculation_mid|speculation
+assessment for|speculation_mid|speculation
+monitor for|speculation_mid|speculation
+monitored for|speculation_mid|speculation
+monitoring for|speculation_mid|speculation
+monitors for|speculation_mid|speculation
+seriologies for|speculation_mid|speculation
+seriology for|speculation_mid|speculation
+work up for|speculation_mid|speculation
+workup for|speculation_mid|speculation

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/models/cue.model
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/models/cue.model?rev=1588552&view=auto
==============================================================================
Binary file - no diff available.

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/models/cue.model
------------------------------------------------------------------------------
    svn:mime-type = application/octet-stream

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/models/featureFile11b
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/models/featureFile11b?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/models/featureFile11b (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/assertion/models/featureFile11b Fri Apr 18 19:47:21 2014
@@ -0,0 +1,12 @@
+conceptUnigrams
+wordLeftFeature
+wordRightFeature
+zone
+cueWord
+cue
+concepts
+#statusRuleMixNMatchFeature
+#cueWordOrderingsLeft
+conceptPseudoHeadFeature
+conceptTextFeature
+cueWordValue



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