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Posted to commits@ctakes.apache.org by se...@apache.org on 2022/11/30 15:54:52 UTC
svn commit: r1905648 [37/37] - in /ctakes/ctakes-models/trunk: ./ .idea/ ctakes-assertion-models/ ctakes-assertion-models/src/ ctakes-assertion-models/src/main/ ctakes-assertion-models/src/main/resources/ ctakes-assertion-models/src/main/resources/org/...
Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/LICENSE
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/LICENSE?rev=1905648&view=auto
==============================================================================
--- ctakes/ctakes-models/trunk/ctakes-temporal-models/LICENSE (added)
+++ ctakes/ctakes-models/trunk/ctakes-temporal-models/LICENSE Wed Nov 30 15:54:26 2022
@@ -0,0 +1,202 @@
+
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Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/pom.xml?rev=1905648&view=auto
==============================================================================
--- ctakes/ctakes-models/trunk/ctakes-temporal-models/pom.xml (added)
+++ ctakes/ctakes-models/trunk/ctakes-temporal-models/pom.xml Wed Nov 30 15:54:26 2022
@@ -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-models</artifactId>
+ <version>5.0.0-SNAPSHOT</version>
+ </parent>
+ <artifactId>ctakes-temporal-models</artifactId>
+ <name>ctakes-temporal models</name>
+ <description>Machine Learning models for ctakes-temporal</description>
+</project>
Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/eventDict.txt
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/eventDict.txt?rev=1905648&view=auto
==============================================================================
--- ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/eventDict.txt (added)
+++ ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/eventDict.txt Wed Nov 30 15:54:26 2022
@@ -0,0 +1,91 @@
+ibuprofen,1
+hypaque,1
+tenormin,1
+celexa,1
+tylenol,1
+betamethasone dipropionate,1
+amoxicillin,1
+finasteride,1
+aspirin,1
+zetia,1
+acetaminophen,1
+maxzide,1
+furosemide,1
+neurontin,1
+cardizem la,1
+cephalexin,1
+prednisone,1
+methylprednisolone,1
+cardizem,1
+fosamax,1
+coumadin,1
+lipitor,1
+folic acid,1
+ezetimibe,1
+xeloda,1
+simvastatin,1
+imodium,1
+lisinopril,1
+penicillin,1
+lantus,1
+vibramycin,1
+keflex,1
+norvasc,1
+xanax,1
+keppra,1
+zestril,1
+proscar,1
+cardura,1
+insulin,1
+hydrochlorothiazide,1
+nitroglycerin,1
+spiriva,1
+synthroid,1
+prilosec,1
+penicillin v potassium,1
+oxaliplatin,1
+zocor,1
+medrol,1
+coreg,1
+cozaar,1
+metoprolol tartrate,1
+progesterone,1
+levofloxacin,1
+lopressor,1
+amoxil,1
+trimethoprim,1
+alprazolam,1
+lasix,1
+albuterol,1
+vicodin,1
+omeprazole,1
+levaquin,1
+fluorouracil,1
+doxycycline,1
+carvedilol,1
+miralax,1
+levoxyl,1
+remeron,1
+penicillin v,1
+roxicodone,1
+nitrofurantoin,1
+triamterene,1
+digoxin,1
+vitamin a,1
+atenolol,1
+motrin,1
+gabapentin,1
+flagyl,1
+cipro,1
+patanol,1
+capecitabine,1
+today,1
+vitamin d,1
+lovenox,1
+fragmin,1
+mirtazapine,1
+sulfamethoxazole,1
+lansoprazole,1
+prevacid,1
+betamethasone,1
+piperacillin,1
\ No newline at end of file
Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/contextualmodality/model.jar
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/contextualmodality/model.jar?rev=1905648&view=auto
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Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/doctimerel/model.jar
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/doctimerel/model.jar?rev=1905648&view=auto
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svn:mime-type = application/octet-stream
Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventannotator/model.jar
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventannotator/model.jar?rev=1905648&view=auto
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Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventevent/Event_Event_UMLS_doubleFilter_useSystemEvents.txt
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventevent/Event_Event_UMLS_doubleFilter_useSystemEvents.txt?rev=1905648&view=auto
==============================================================================
--- ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventevent/Event_Event_UMLS_doubleFilter_useSystemEvents.txt (added)
+++ ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventevent/Event_Event_UMLS_doubleFilter_useSystemEvents.txt Wed Nov 30 15:54:26 2022
@@ -0,0 +1,35 @@
+a)No closure on gold::Closure on System::Recall Mode
+P R F1 #gold #system #correct
+0.351 0.572 0.435 584 951 334 OVERALL
+0.154 0.154 0.154 39 39 6 BEFORE
+0.111 0.067 0.083 15 9 1 BEGINS-ON
+0.611 0.708 0.656 390 452 276 CONTAINS
+0 0 0 1 9 0 ENDS-ON
+0.115 0.367 0.176 139 442 51 OVERLAP
+
+b) No closure on System::Closure on Gold::Precision Mode
+P R F1 #gold #system #correct
+0.487 0.438 0.461 765 688 335 OVERALL
+0.176 0.125 0.146 48 34 6 BEFORE
+0.111 0.063 0.08 16 9 1 BEGINS-ON
+0.613 0.707 0.656 392 452 277 CONTAINS
+1 0 0 16 0 0 ENDS-ON
+0.264 0.174 0.21 293 193 51 OVERLAP
+
+c) Final Score:
+P R F
+0.487 0.572 0.526088763 OVERALL
+0.176 0.154 0.164266667 BEFORE
+0.111 0.067 0.083561798 BEGINS-ON
+0.613 0.708 0.657084027 CONTAINS
+1 0 0 ENDS-ON
+0.264 0.367 0.307093502 OVERLAP
+d) Closure on train::No closure onTest::PlainMode
+P R F1 #gold #system #correct
+0.419 0.493 0.453 584 688 288 OVERALL
+0.176 0.154 0.164 39 34 6 BEFORE
+0.111 0.067 0.083 15 9 1 BEGINS-ON
+0.611 0.708 0.656 390 452 276 CONTAINS
+1 0 0 1 0 0 ENDS-ON
+0.026 0.036 0.03 139 193 5 OVERLAP
+
Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventevent/READEME.txt
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventevent/READEME.txt?rev=1905648&view=auto
==============================================================================
--- ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventevent/READEME.txt (added)
+++ ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventevent/READEME.txt Wed Nov 30 15:54:26 2022
@@ -0,0 +1,10 @@
+Models are trained on THYME patient sets: 28-127
+Training data: Mode 8, residue 0-3
+Testing data: Mode 8, residue 4 and 5
+
+UMLS entities, whose spans overlap with gold Events, were extracted to boost training data
+UMLS entities were not extracted for testing data. For testing data, only gold events were used for evaluation.
+
+Both arguments of event-event relations are required to be valid medical terms (i.e. be one of the UMLS semantic types).
+We show test results for event-time relations, in which events were not required to be valid medical terms.
+Results for event-time relations, in which event arguments are requried to be valid medical terms, were also shown here. Final event-time model is UMLS-filtered.
\ No newline at end of file
Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventevent/model.jar
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventevent/model.jar?rev=1905648&view=auto
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Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventtime/Event_Time_no_UMLS_filter.txt
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventtime/Event_Time_no_UMLS_filter.txt?rev=1905648&view=auto
==============================================================================
--- ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventtime/Event_Time_no_UMLS_filter.txt (added)
+++ ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventtime/Event_Time_no_UMLS_filter.txt Wed Nov 30 15:54:26 2022
@@ -0,0 +1,36 @@
+a)No closure on gold::Closure on System::Recall Mode
+P R F1 #gold #system #correct
+0.459 0.64 0.535 1229 1715 787 OVERALL
+0.048 0.081 0.061 37 62 3 BEFORE
+0.207 0.143 0.169 42 29 6 BEGINS-ON
+0.576 0.777 0.662 977 1317 759 CONTAINS
+0.214 0.214 0.214 28 28 6 ENDS-ON
+0.047 0.09 0.061 145 279 13 OVERLAP
+
+b) No closure on System::Closure on Gold::Precision Mode
+P R F1 #gold #system #correct
+0.617 0.399 0.485 2379 1540 950 OVERALL
+0.052 0.039 0.044 77 58 3 BEFORE
+0.353 0.086 0.138 70 17 6 BEGINS-ON
+0.672 0.727 0.698 1216 1316 884 CONTAINS
+0.5 0.092 0.156 65 12 6 ENDS-ON
+0.372 0.054 0.094 951 137 51 OVERLAP
+
+c) Final Score:
+P R F
+0.617 0.64 0.628289578 OVERALL
+0.052 0.081 0.063338346 BEFORE
+0.353 0.143 0.203544355 BEGINS-ON
+0.672 0.777 0.720695652 CONTAINS
+0.5 0.214 0.299719888 ENDS-ON
+0.372 0.09 0.144935065 OVERLAP
+
+d) Closure on train::No closure onTest::PlainMode
+P R F1 #gold #system#correct
+0.508 0.637 0.566 1229 1540 783 OVERALL
+0.052 0.081 0.063 37 58 3 BEFORE
+0.353 0.143 0.203 42 17 6 BEGINS-ON
+0.577 0.777 0.662 977 1316 759 CONTAINS
+0.5 0.214 0.3 28 12 6 ENDS-ON
+0.066 0.062 0.064 145 137 9 OVERLAP
+
Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventtime/Event_Time_with_UMLS_filter.txt
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventtime/Event_Time_with_UMLS_filter.txt?rev=1905648&view=auto
==============================================================================
--- ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventtime/Event_Time_with_UMLS_filter.txt (added)
+++ ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventtime/Event_Time_with_UMLS_filter.txt Wed Nov 30 15:54:26 2022
@@ -0,0 +1,36 @@
+a)No closure on gold::Closure on System::Recall Mode
+P R F1 #gold #system #correct
+0.358 0.628 0.456 549 964 345 OVERALL
+0 0 0 14 7 0 BEFORE
+0.5 0.045 0.083 22 2 1 BEGINS-ON
+0.661 0.746 0.701 437 493 326 CONTAINS
+0 0 0 7 2 0 ENDS-ON
+0.039 0.261 0.068 69 460 18 OVERLAP
+
+b) No closure on System::Closure on Gold::Precision Mode
+P R F1 #gold #system #correct
+0.594 0.256 0.357 1702 732 435 OVERALL
+0 0 0 51 7 0 BEFORE
+0.5 0.02 0.038 50 2 1 BEGINS-ON
+0.716 0.506 0.593 698 493 353 CONTAINS
+1 0 0 43 0 0 ENDS-ON
+0.352 0.094 0.149 860 230 81 OVERLAP
+
+c) Final Score:
+P R F
+0.594 0.628 0.610527005 OVERALL
+0 0 #DIV/0! BEFORE
+0.5 0.045 0.082568807 BEGINS-ON
+0.716 0.746 0.730692202 CONTAINS
+1 0 0 ENDS-ON
+0.352 0.261 0.299745514 OVERLAP
+
+d) Closure on train::No closure onTest::PlainMode
+P R F1 #gold #system#correct
+0.462 0.616 0.528 549 732 338 OVERALL
+0 0 0 14 7 0 BEFORE
+0.5 0.045 0.083 22 2 1 BEGINS-ON
+0.661 0.746 0.701 437 493 326 CONTAINS
+1 0 0 7 0 0 ENDS-ON
+0.048 0.159 0.074 69 230 11 OVERLAP
+
Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventtime/READEME.txt
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventtime/READEME.txt?rev=1905648&view=auto
==============================================================================
--- ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventtime/READEME.txt (added)
+++ ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventtime/READEME.txt Wed Nov 30 15:54:26 2022
@@ -0,0 +1,10 @@
+Models are trained on THYME patient sets: 28-127
+Training data: Mode 8, residue 0-3
+Testing data: Mode 8, residue 4 and 5
+
+UMLS entities, whose spans overlap with gold Events, were extracted to boost training data
+UMLS entities were not extracted for testing data. For testing data, only gold events were used for evaluation.
+
+Both arguments of event-event relations are required to be valid medical terms (i.e. be one of the UMLS semantic types).
+We show test results for event-time relations, in which events were not required to be valid medical terms.
+Results for event-time relations, in which event arguments are requried to be valid medical terms, were also shown here. Final event-time model is UMLS-filtered.
\ No newline at end of file
Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventtime/model.jar
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/eventtime/model.jar?rev=1905648&view=auto
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Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/salience/model.jar
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/salience/model.jar?rev=1905648&view=auto
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Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/section/DefaultMedSections.txt
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/section/DefaultMedSections.txt?rev=1905648&view=auto
==============================================================================
--- ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/section/DefaultMedSections.txt (added)
+++ ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/section/DefaultMedSections.txt Wed Nov 30 15:54:26 2022
@@ -0,0 +1,16 @@
+Medications
+Medications Outside Hospital
+Discharge Instructions
+Emergency Department Course
+Medication History
+Input Fluids
+Medications By Type
+Substance Abuse Treatment
+Medications at Transfer
+Instructions
+Current Antibiotics
+Plan
+Labs
+Diet
+Vaccinations
+Past Medications
Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/section/ccda_sections.txt
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/section/ccda_sections.txt?rev=1905648&view=auto
==============================================================================
--- ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/section/ccda_sections.txt (added)
+++ ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/section/ccda_sections.txt Wed Nov 30 15:54:26 2022
@@ -0,0 +1,12 @@
+# This file is used by ctakes-core/sectionizer
+# It uses rules and RegEx to match the section headers
+# It is derived from the Consolidated CDA/HL7 standard
+# http://bluebuttonplus.org/healthrecords.html
+# http://cdatools.org/infocenter/index.jsp
+# The format is as follows:
+# HL7 template id,LOINC Section Code,n list of header names
+# Custom ones can be added to the below mapping file
+# By Default,they are case insenstive and spaces trimmed.
+
+history,1,HISTORY OF PRESENT ILLNESS,brief history of physical illness,history of present illness,history of the present illness,HISTORY,HISTORY AND REASON FOR HOSPITALIZATION,HISTORY AND REASON FOR ADMISSION,PRESENT ILLNESS,HPI,Service,OPERATIONS \/ PROCEDURES,OTHER POSTPARTUM THERAPIES
+course,2,HOSPITAL COURSE,HOSPITAL COURSE \( include complications if any \),Brief Hospital Course,HOSPITAL COURSE BY SYSTEM,HOSPITAL COURSE BY SYSTEMS,BRIEF RESUME OF HOSPITAL COURSE,SUMMARY OF HOSPITAL COURSE BY SYSTEMS,HOSPITAL COURSE BY SYSTEMS INCLUDING PERTINENT LABORATORY DATA,SUMMARY OF HOSPITAL COURSE BY ISSUES-SYSTEM,SUMMARY OF HOSPITAL COURSE,HOSPITAL COURSE AND TREATMENT,HOSPITAL COURSE OVER THESE PREVIOUS DAYS
\ No newline at end of file
Added: ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/timeannotator/model.jar
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/ctakes-temporal-models/src/main/resources/org/apache/ctakes/temporal/models/timeannotator/model.jar?rev=1905648&view=auto
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Added: ctakes/ctakes-models/trunk/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/ctakes-models/trunk/pom.xml?rev=1905648&view=auto
==============================================================================
--- ctakes/ctakes-models/trunk/pom.xml (added)
+++ ctakes/ctakes-models/trunk/pom.xml Wed Nov 30 15:54:26 2022
@@ -0,0 +1,507 @@
+<?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>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-models</artifactId>
+ <version>5.0.0-SNAPSHOT</version>
+ <packaging>pom</packaging>
+ <name>Apache cTAKES Models</name>
+ <url>http://ctakes.apache.org</url>
+ <inceptionYear>2012</inceptionYear>
+ <scm>
+ <!-- In child modules, Maven will append ${artifactId} to the following
+ URLs -->
+ <connection>scm:svn:https://svn.apache.org/repos/asf/ctakes/ctakes-models/trunk</connection>
+ <developerConnection>scm:svn:https://svn.apache.org/repos/asf/ctakes/ctakes-models/trunk</developerConnection>
+ <url>https://svn.apache.org/repos/asf/ctakes/ctakes-models/trunk</url>
+ </scm>
+ <issueManagement>
+ <system>jira</system>
+ <url>https://issues.apache.org/jira/browse/ctakes</url>
+ </issueManagement>
+ <!-- <ciManagement>
+ <system>jenkins</system>
+ <url>https://builds.apache.org/job/ctakes-trunk/</url>
+ </ciManagement>
+ -->
+ <mailingLists>
+ <mailingList>
+ <name>Apache cTAKES Users</name>
+ <subscribe>user-subscribe@ctakes.apache.org</subscribe>
+ <unsubscribe>user-unsubscribe@ctakes.apache.org</unsubscribe>
+ <post>user@ctakes.apache.org</post>
+ <archive>http://mail-archives.apache.org/mod_mbox/ctakes-user/</archive>
+ </mailingList>
+
+ <mailingList>
+ <name>Apache cTAKES Developers</name>
+ <subscribe>dev-subscribe@ctakes.apache.org</subscribe>
+ <unsubscribe>dev-unsubscribe@ctakes.apache.org</unsubscribe>
+ <post>dev@ctakes.apache.org</post>
+ <archive>http://mail-archives.apache.org/mod_mbox/ctakes-dev/</archive>
+ </mailingList>
+
+ <mailingList>
+ <name>Apache cTAKES Commits</name>
+ <subscribe>commits-subscribe@ctakes.apache.org</subscribe>
+ <unsubscribe>commits-unsubscribe@ctakes.apache.org</unsubscribe>
+ <archive>http://mail-archives.apache.org/mod_mbox/ctakes-commits/</archive>
+ </mailingList>
+
+ <mailingList>
+ <name>Apache cTAKES Notifications</name>
+ <subscribe>notifications-subscribe@ctakes.apache.org</subscribe>
+ <unsubscribe>notifications-unsubscribe@ctakes.apache.org</unsubscribe>
+ <archive>http://mail-archives.apache.org/mod_mbox/ctakes-notifications/</archive>
+ </mailingList>
+ </mailingLists>
+
+ <properties>
+ <!-- dependencies -->
+ <ant.version>1.9.2</ant.version>
+ <maven-antrun-plugin.version>3.1.0</maven-antrun-plugin.version>
+ <maven-assembly-plugin.version>3.4.2</maven-assembly-plugin.version>
+ <maven-failsafe-plugin.version>2.20.1</maven-failsafe-plugin.version>
+ <maven-surefire-plugin.version>3.0.0-M7</maven-surefire-plugin.version>
+ <maven-war-plugin.version>3.3.2</maven-war-plugin.version>
+ <maven-license-plugin.version>1.9.0</maven-license-plugin.version>
+ <maven-clean-plugin.version>3.2.0</maven-clean-plugin.version>
+ <maven-compiler-plugin.version>3.10.1</maven-compiler-plugin.version>
+ <maven-deploy-plugin.version>3.0.0</maven-deploy-plugin.version>
+ <maven-gpg-plugin.version>3.0.1</maven-gpg-plugin.version>
+ <maven-install-plugin.version>3.0.1</maven-install-plugin.version>
+ <maven-jar-plugin.version>3.3.0</maven-jar-plugin.version>
+ <maven-javadoc-plugin.version>3.4.1</maven-javadoc-plugin.version>
+ <maven-dependency-plugin.version>3.3.0</maven-dependency-plugin.version>
+ <maven-site-plugin.version>4.0.0-M3</maven-site-plugin.version>
+ <maven-source-plugin.version>3.2.1</maven-source-plugin.version>
+ <apache-rat-plugin.version>0.15</apache-rat-plugin.version>
+ <properties-maven-plugin.version>1.1.0</properties-maven-plugin.version>
+ <maven-remote-resources-plugin.version>3.0.0</maven-remote-resources-plugin.version>
+
+ <!-- project specific conventions -->
+ <maven.compiler.source>1.8</maven.compiler.source>
+ <maven.compiler.target>1.8</maven.compiler.target>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <maven.build.timestamp.format>yyyy-MM-dd HH:mm</maven.build.timestamp.format>
+ </properties>
+
+ <parent>
+ <groupId>org.apache</groupId>
+ <artifactId>apache</artifactId>
+ <version>13</version>
+ </parent>
+
+ <modules>
+ <module>ctakes-assertion-models</module>
+ <module>ctakes-chunker-models</module>
+ <module>ctakes-constituency-parser-models</module>
+ <module>ctakes-core-models</module>
+ <module>ctakes-coreference-models</module>
+ <module>ctakes-dependency-parser-models</module>
+ <module>ctakes-dependency-parser-models-clear</module>
+ <module>ctakes-pos-tagger-models</module>
+ <module>ctakes-relation-extractor-models</module>
+ <module>ctakes-side-effect-models</module>
+ <module>ctakes-smoking-status-models</module>
+ <module>ctakes-temporal-models</module>
+ </modules>
+ <dependencyManagement>
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-core-models</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-pos-tagger-models</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-chunker-models</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-assertion-models</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-constituency-parser-models</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-coreference-models</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-side-effect-models</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-smoking-status-models</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dependency-parser-models</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dependency-parser-models-clear</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-relation-extractor-models</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-temporal-models</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+ </dependencyManagement>
+ <build>
+ <!-- It's good practice to explicitly declare versions for all plugins -->
+ <pluginManagement>
+ <plugins>
+ <!-- TODO: remove dependency upon Apache Ant -->
+ <plugin>
+ <artifactId>maven-antrun-plugin</artifactId>
+ <version>${maven-antrun-plugin.version}</version>
+ </plugin>
+ <plugin>
+ <groupId>com.mycila.maven-license-plugin</groupId>
+ <artifactId>maven-license-plugin</artifactId>
+ <version>${maven-license-plugin.version}</version>
+ <configuration>
+ <header>ctakes-distribution/src/main/config/license_header.txt</header>
+ <excludes>
+ <!-- We're disabling .txt files for now because some Annotators may
+ not be able to handle standard comments in text files. This may break name
+ values pairs such as stopWords.txt -->
+ <exclude>**.txt</exclude>
+ </excludes>
+ <useDefaultMapping>false</useDefaultMapping>
+ <quiet>false</quiet>
+ <failIfMissing>false</failIfMissing>
+ <mapping>
+ <java>JAVADOC_STYLE</java>
+ <groovy>JAVADOC_STYLE</groovy>
+ <js>JAVADOC_STYLE</js>
+ <css>JAVADOC_STYLE</css>
+ <xml>XML_STYLE</xml>
+ <dtd>XML_STYLE</dtd>
+ <xsd>XML_STYLE</xsd>
+ <html>XML_STYLE</html>
+ <htm>XML_STYLE</htm>
+ <xsl>XML_STYLE</xsl>
+ <fml>XML_STYLE</fml>
+ <apt>DOUBLETILDE_STYLE</apt>
+ <properties>SCRIPT_STYLE</properties>
+ <sh>SCRIPT_STYLE</sh>
+ <!-- <txt>TEXT</txt> -->
+ <bat>BATCH</bat>
+ <cmd>BATCH</cmd>
+ <sql>DOUBLEDASHES_STYLE</sql>
+ <jsp>DYNASCRIPT_STYLE</jsp>
+ <ftl>FTL</ftl>
+ <xhtml>XML_STYLE</xhtml>
+ <vm>SHARPSTAR_STYLE</vm>
+ <jspx>XML_STYLE</jspx>
+ </mapping>
+ <properties>
+ <owner>Apache Software Foundation</owner>
+ <year>${project.inceptionYear}</year>
+ <email>dev@ctakes.apache.org</email>
+ </properties>
+ <strictCheck>true</strictCheck>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <version>${maven-assembly-plugin.version}</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-clean-plugin</artifactId>
+ <version>${maven-clean-plugin.version}</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <version>${maven-compiler-plugin.version}</version>
+ <configuration>
+ <source>1.8</source>
+ <target>1.8</target>
+ <compilerArgument>-Xlint</compilerArgument>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-deploy-plugin</artifactId>
+ <version>${maven-deploy-plugin.version}</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-gpg-plugin</artifactId>
+ <version>${maven-gpg-plugin.version}</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-install-plugin</artifactId>
+ <version>${maven-install-plugin.version}</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-jar-plugin</artifactId>
+ <version>${maven-jar-plugin.version}</version>
+ <configuration>
+ <includes>
+ <!-- Resources will be copied by the assembly
+ No need for it to be inside the jar
+ <include>**/*.class</include>
+ <include>**/types/*.xml</include>
+ <include>**/META-INF/**</include>
+ -->
+ </includes>
+ <archive>
+ <manifest>
+ <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
+ </manifest>
+ <manifestEntries>
+ <Implementation-Build-Date>${maven.build.timestamp}</Implementation-Build-Date>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-javadoc-plugin</artifactId>
+ <version>${maven-javadoc-plugin.version}</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-resources-plugin</artifactId>
+ <version>2.5</version>
+ <!-- <version>${maven-resources-plugin.version}}</version>-->
+ </plugin>
+ <plugin>
+ <artifactId>maven-dependency-plugin</artifactId>
+ <version>${maven-dependency-plugin.version}</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-site-plugin</artifactId>
+ <version>${maven-site-plugin.version}</version>
+ </plugin>
+ <plugin>
+ <artifactId>maven-source-plugin</artifactId>
+ <version>${maven-source-plugin.version}</version>
+ </plugin>
+ <!-- Maven expects tests to start or end with "Test", not "Tests", so
+ explicitly include files ending in "Tests" -->
+ <plugin>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>${maven-surefire-plugin.version}</version>
+ <configuration>
+ <includes>
+ <include>**/Test*.java</include>
+ <include>**/*Test.java</include>
+ <include>**/*Tests.java</include>
+ <include>**/*TestCase.java</include>
+ </includes>
+ <argLine>-Xmx3g</argLine>
+ <forkedProcessTimeoutInSeconds>900</forkedProcessTimeoutInSeconds>
+ <additionalClasspathElements>
+ <additionalClasspathElement>ctakes-assertion-models/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-chunker-models/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-constituency-parser-models/src/main/resources
+ </additionalClasspathElement>
+ <additionalClasspathElement>ctakes-core-models/src/main/resources</additionalClasspathElement>
+ <additionalClasspathElement>ctakes-coreference-models/src/main/resources
+ </additionalClasspathElement>
+ <additionalClasspathElement>ctakes-dependency-parser-models/src/main/resources
+ </additionalClasspathElement>
+ <additionalClasspathElement>ctakes-dependency-parser-models-clear/src/main/resources
+ </additionalClasspathElement>
+ <additionalClasspathElement>ctakes-pos-tagger-models/src/main/resources
+ </additionalClasspathElement>
+ <additionalClasspathElement>ctakes-relation-extractor-models/src/main/resources
+ </additionalClasspathElement>
+ <additionalClasspathElement>ctakes-side-effect-models/src/main/resources
+ </additionalClasspathElement>
+ <additionalClasspathElement>ctakes-smoking-status-models/src/main/resources
+ </additionalClasspathElement>
+ <additionalClasspathElement>ctakes-temporal-models/src/main/resources</additionalClasspathElement>
+ </additionalClasspathElements>
+ </configuration>
+ </plugin>
+
+ <!-- apache-rat:check validate release -->
+ <plugin>
+ <groupId>org.apache.rat</groupId>
+ <artifactId>apache-rat-plugin</artifactId>
+ <version>${apache-rat-plugin.version}</version>
+ <configuration>
+ <excludes>
+ <!-- generated directories -->
+ <exclude>**/target/**/*</exclude>
+ <exclude>resources/**/*</exclude>
+ <!-- version control -->
+ <exclude>.git/**/*</exclude>
+ <exclude>.gitignore</exclude>
+ <!-- Eclipse files -->
+ <exclude>**/.*</exclude>
+ <exclude>**/.settings/*</exclude>
+ <exclude>**/eclipse-classes/**/*</exclude>
+ <!-- IDEA IntelliJ files -->
+ <exclude>**/*.iml</exclude>
+ <exclude>**/*.ipr</exclude>
+ <exclude>**/*.iws</exclude>
+ <exclude>**/.idea/**/*</exclude>
+ <!-- File generated by maven-release-plugin -->
+ <exclude>release.properties</exclude>
+ <!-- Exclude bin/model resources -->
+ <!-- TODO: do not exclude resources. Rat should exclude binaries by default -->
+ <exclude>**/src/main/resources/**</exclude>
+ <exclude>**/src/test/resources/**</exclude>
+ <exclude>**/META-INF/org.uimafit/types.txt</exclude>
+ <exclude>**/MANIFEST.MF</exclude>
+ <!-- Exclude test data files -->
+ <exclude>**/data/test/**</exclude>
+ <exclude>**/data/**</exclude>
+ <exclude>**/output/**</exclude>
+ <exclude>**/sample_note.txt</exclude>
+ </excludes>
+ <numUnapprovedLicenses>0</numUnapprovedLicenses>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.eclipse.m2e</groupId>
+ <artifactId>lifecycle-mapping</artifactId>
+ <version>1.0.0</version>
+ <configuration>
+ <lifecycleMappingMetadata>
+ <pluginExecutions>
+ <pluginExecution>
+ <!--
+ This is needed to execute/unpack resources in m2e eclipse ide
+ Currently used in the ctakes-dictionary-lookup project
+ -->
+ <pluginExecutionFilter>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-dependency-plugin</artifactId>
+ <versionRange>${maven-dependency-plugin.version}</versionRange>
+ <goals>
+ <goal>unpack-dependencies</goal>
+ </goals>
+ </pluginExecutionFilter>
+ <action>
+ <execute>
+ <runOnIncremental>true</runOnIncremental>
+ </execute>
+ </action>
+ </pluginExecution>
+ <pluginExecution>
+ <!--
+ Ignore the Maven remote resources plugin in Eclipse. We don't use it from Eclipse,
+ and it causes a warning if m2e is not configured to ignore it as below.
+ -->
+ <pluginExecutionFilter>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-remote-resources-plugin</artifactId>
+ <versionRange>${maven-remote-resources-plugin.version}</versionRange>
+ <goals>
+ <goal>process</goal>
+ </goals>
+ </pluginExecutionFilter>
+ <action>
+ <ignore/>
+ </action>
+ </pluginExecution>
+ </pluginExecutions>
+ </lifecycleMappingMetadata>
+ </configuration>
+ </plugin>
+ <!-- exec-maven-plugin -->
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>exec-maven-plugin</artifactId>
+ <version>${exec-maven-plugin.version}</version>
+ <executions>
+ <execution>
+ <phase>compile</phase>
+ <goals>
+ <goal>java</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <executable>java</executable>
+ <includeProjectDependencies>true</includeProjectDependencies>
+ <includePluginDependencies>true</includePluginDependencies>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.uima</groupId>
+ <artifactId>jcasgen-maven-plugin</artifactId>
+ <version>${uimaj.version}</version>
+ </plugin>
+ </plugins>
+ </pluginManagement>
+ </build>
+ <profiles>
+ <profile>
+ <id>disable-java8-doclint</id>
+ <activation>
+ <jdk>[1.8,)</jdk>
+ </activation>
+ <properties>
+ <additionalparam>-Xdoclint:none</additionalparam>
+ </properties>
+ </profile>
+ <!-- START SNIPPET: release-profile -->
+ <!-- !IMPORTANT: Overrides the official org.apache:apache (parent pom) -->
+ <profile>
+ <id>apache-release</id>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>${maven-surefire-plugin.version}</version>
+ <configuration>
+ <environmentVariables>
+ <ctakes.umlsuser>CHANGE_ME</ctakes.umlsuser>
+ </environmentVariables>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+ </profile>
+ <!-- END SNIPPET: release-profile -->
+ </profiles>
+</project>