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From chen...@apache.org
Subject svn commit: r1463641 [35/42] - in /ctakes/trunk: ctakes-assertion-res/ ctakes-assertion-res/.settings/ ctakes-assertion-res/src/ ctakes-assertion-res/src/main/ ctakes-assertion-res/src/main/resources/ ctakes-assertion-res/src/main/resources/org/ ctakes...
Date Tue, 02 Apr 2013 17:44:41 GMT
Added: ctakes/trunk/ctakes-pos-tagger-res/.settings/org.eclipse.jdt.core.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger-res/.settings/org.eclipse.jdt.core.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-pos-tagger-res/.settings/org.eclipse.jdt.core.prefs (added)
+++ ctakes/trunk/ctakes-pos-tagger-res/.settings/org.eclipse.jdt.core.prefs Tue Apr  2 17:41:30
2013
@@ -0,0 +1,88 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.annotation.missingNonNullByDefaultAnnotation=ignore
+org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jdt.annotation.NonNull
+org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annotation.NonNullByDefault
+org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nullable
+org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.annotationSuperInterface=warning
+org.eclipse.jdt.core.compiler.problem.autoboxing=ignore
+org.eclipse.jdt.core.compiler.problem.comparingIdentical=warning
+org.eclipse.jdt.core.compiler.problem.deadCode=warning
+org.eclipse.jdt.core.compiler.problem.deprecation=warning
+org.eclipse.jdt.core.compiler.problem.deprecationInDeprecatedCode=disabled
+org.eclipse.jdt.core.compiler.problem.deprecationWhenOverridingDeprecatedMethod=disabled
+org.eclipse.jdt.core.compiler.problem.discouragedReference=warning
+org.eclipse.jdt.core.compiler.problem.emptyStatement=warning
+org.eclipse.jdt.core.compiler.problem.explicitlyClosedAutoCloseable=warning
+org.eclipse.jdt.core.compiler.problem.fallthroughCase=ignore
+org.eclipse.jdt.core.compiler.problem.fatalOptionalError=disabled
+org.eclipse.jdt.core.compiler.problem.fieldHiding=warning
+org.eclipse.jdt.core.compiler.problem.finalParameterBound=warning
+org.eclipse.jdt.core.compiler.problem.finallyBlockNotCompletingNormally=warning
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.problem.hiddenCatchBlock=warning
+org.eclipse.jdt.core.compiler.problem.includeNullInfoFromAsserts=disabled
+org.eclipse.jdt.core.compiler.problem.incompatibleNonInheritedInterfaceMethod=warning
+org.eclipse.jdt.core.compiler.problem.incompleteEnumSwitch=warning
+org.eclipse.jdt.core.compiler.problem.indirectStaticAccess=warning
+org.eclipse.jdt.core.compiler.problem.localVariableHiding=warning
+org.eclipse.jdt.core.compiler.problem.methodWithConstructorName=warning
+org.eclipse.jdt.core.compiler.problem.missingDefaultCase=ignore
+org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=warning
+org.eclipse.jdt.core.compiler.problem.missingEnumCaseDespiteDefault=disabled
+org.eclipse.jdt.core.compiler.problem.missingHashCodeMethod=warning
+org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotation=warning
+org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotationForInterfaceMethodImplementation=disabled
+org.eclipse.jdt.core.compiler.problem.missingSerialVersion=warning
+org.eclipse.jdt.core.compiler.problem.missingSynchronizedOnInheritedMethod=warning
+org.eclipse.jdt.core.compiler.problem.noEffectAssignment=warning
+org.eclipse.jdt.core.compiler.problem.noImplicitStringConversion=warning
+org.eclipse.jdt.core.compiler.problem.nonExternalizedStringLiteral=ignore
+org.eclipse.jdt.core.compiler.problem.nullAnnotationInferenceConflict=error
+org.eclipse.jdt.core.compiler.problem.nullReference=warning
+org.eclipse.jdt.core.compiler.problem.nullSpecViolation=error
+org.eclipse.jdt.core.compiler.problem.nullUncheckedConversion=warning
+org.eclipse.jdt.core.compiler.problem.overridingPackageDefaultMethod=warning
+org.eclipse.jdt.core.compiler.problem.parameterAssignment=ignore
+org.eclipse.jdt.core.compiler.problem.possibleAccidentalBooleanAssignment=warning
+org.eclipse.jdt.core.compiler.problem.potentialNullReference=warning
+org.eclipse.jdt.core.compiler.problem.potentiallyUnclosedCloseable=warning
+org.eclipse.jdt.core.compiler.problem.rawTypeReference=warning
+org.eclipse.jdt.core.compiler.problem.redundantNullAnnotation=warning
+org.eclipse.jdt.core.compiler.problem.redundantNullCheck=warning
+org.eclipse.jdt.core.compiler.problem.redundantSpecificationOfTypeArguments=warning
+org.eclipse.jdt.core.compiler.problem.redundantSuperinterface=warning
+org.eclipse.jdt.core.compiler.problem.reportMethodCanBePotentiallyStatic=ignore
+org.eclipse.jdt.core.compiler.problem.reportMethodCanBeStatic=warning
+org.eclipse.jdt.core.compiler.problem.specialParameterHidingField=disabled
+org.eclipse.jdt.core.compiler.problem.staticAccessReceiver=warning
+org.eclipse.jdt.core.compiler.problem.suppressOptionalErrors=disabled
+org.eclipse.jdt.core.compiler.problem.suppressWarnings=enabled
+org.eclipse.jdt.core.compiler.problem.syntheticAccessEmulation=warning
+org.eclipse.jdt.core.compiler.problem.typeParameterHiding=warning
+org.eclipse.jdt.core.compiler.problem.unavoidableGenericTypeProblems=enabled
+org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
+org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
+org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unnecessaryElse=warning
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+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownException=warning
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionExemptExceptionAndThrowable=enabled
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionIncludeDocCommentReference=enabled
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionWhenOverriding=disabled
+org.eclipse.jdt.core.compiler.problem.unusedImport=warning
+org.eclipse.jdt.core.compiler.problem.unusedLabel=warning
+org.eclipse.jdt.core.compiler.problem.unusedLocal=warning
+org.eclipse.jdt.core.compiler.problem.unusedObjectAllocation=warning
+org.eclipse.jdt.core.compiler.problem.unusedParameter=warning
+org.eclipse.jdt.core.compiler.problem.unusedParameterIncludeDocCommentReference=enabled
+org.eclipse.jdt.core.compiler.problem.unusedParameterWhenImplementingAbstract=disabled
+org.eclipse.jdt.core.compiler.problem.unusedParameterWhenOverridingConcrete=disabled
+org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
+org.eclipse.jdt.core.compiler.problem.unusedWarningToken=ignore
+org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
+org.eclipse.jdt.core.compiler.source=1.6

Added: ctakes/trunk/ctakes-pos-tagger-res/.settings/org.eclipse.ltk.core.refactoring.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger-res/.settings/org.eclipse.ltk.core.refactoring.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-pos-tagger-res/.settings/org.eclipse.ltk.core.refactoring.prefs (added)
+++ ctakes/trunk/ctakes-pos-tagger-res/.settings/org.eclipse.ltk.core.refactoring.prefs Tue
Apr  2 17:41:30 2013
@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+org.eclipse.ltk.core.refactoring.enable.project.refactoring.history=false

Added: ctakes/trunk/ctakes-pos-tagger-res/.settings/org.eclipse.m2e.core.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger-res/.settings/org.eclipse.m2e.core.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-pos-tagger-res/.settings/org.eclipse.m2e.core.prefs (added)
+++ ctakes/trunk/ctakes-pos-tagger-res/.settings/org.eclipse.m2e.core.prefs Tue Apr  2 17:41:30
2013
@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

Added: ctakes/trunk/ctakes-pos-tagger-res/LICENSE
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger-res/LICENSE?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-pos-tagger-res/LICENSE (added)
+++ ctakes/trunk/ctakes-pos-tagger-res/LICENSE Tue Apr  2 17:41:30 2013
@@ -0,0 +1,202 @@
+
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Added: ctakes/trunk/ctakes-pos-tagger-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger-res/pom.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-pos-tagger-res/pom.xml (added)
+++ ctakes/trunk/ctakes-pos-tagger-res/pom.xml Tue Apr  2 17:41:30 2013
@@ -0,0 +1,32 @@
+<?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.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <parent>
+    <groupId>org.apache.ctakes</groupId>
+    <artifactId>ctakes</artifactId>
+    <version>3.1.0-SNAPSHOT</version>
+  </parent>
+  <artifactId>ctakes-pos-tagger-res</artifactId>
+  <name>Apache cTAKES Resources pos-tagger</name>
+  <description>Resources Project for ctakes-pos-tagger</description>
+</project>
\ No newline at end of file

Added: ctakes/trunk/ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/README
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/README?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/README
(added)
+++ ctakes/trunk/ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/README
Tue Apr  2 17:41:30 2013
@@ -0,0 +1,27 @@
+
+A part-of-speech tagging model and tag dictionary are included with this project.
+
+The model derives from a combination of GENIA, Penn Treebank (Wall Street Journal) and anonymized
+clinical data per Safe Harbor HIPAA guidelines. Prior to model building, the clinical data
was 
+deidentified for patient names to preserve patient confidentiality. Any person name in the
model 
+will originate from non-patient data sources.
+
+
+To build a model of your own, you need to
+
+1) obtain training data - see data/pos/training/README
+2) build a model using the training data. 
+
+After you have obtained training data, you can build a model by running the following:
+
+java opennlp.tools.postag.POSTaggerME <training-data> <model-name> <iterations>
<cutoff>
+where <training-data> is an OpenNLP training data file as described in data/pos/training/README
+      <model-name> The file name of the resulting model.  The name should end with
either '.txt'
+                   (for a plain text model) or '.bin.gz' (for a compressed binary model).
 
+      <iterations> The iterations argument determines how many training iterations
will be 
+                   performed.  The default is 100.  
+      <cutoff>     The cutoff argument determines the minimum number of times a feature
has to be
+                   seen to be considered for inclusion in the model.  The default cutoff
is 5.  
+
+The arguments <iterations> and <cutoff> are, taken together, optional - i.e.
you should provide 
+both or provide neither.  

Added: ctakes/trunk/ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/mayo-pos.zip
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/mayo-pos.zip?rev=1463641&view=auto
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Added: ctakes/trunk/ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/postagger.model.bin.gz
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/postagger.model.bin.gz?rev=1463641&view=auto
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Added: ctakes/trunk/ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/small/postagger.model.bin.gz
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/small/postagger.model.bin.gz?rev=1463641&view=auto
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Added: ctakes/trunk/ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/small/tag.dictionary.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/small/tag.dictionary.txt?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/small/tag.dictionary.txt
(added)
+++ ctakes/trunk/ctakes-pos-tagger-res/src/main/resources/org/apache/ctakes/postagger/models/small/tag.dictionary.txt
Tue Apr  2 17:41:30 2013
@@ -0,0 +1,10 @@
+Use IN
+of IN
+new IN
+biologic IN
+markers IN
+in IN
+the IN
+ovulation IN
+induction IN
+. IN 



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