ctakes-commits mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From seanfi...@apache.org
Subject svn commit: r1765001 [1/2] - in /ctakes/trunk: ./ ctakes-core/src/main/java/org/apache/ctakes/core/cr/ ctakes-examples-res/ ctakes-examples-res/src/ ctakes-examples-res/src/main/ ctakes-examples-res/src/main/resources/ ctakes-examples-res/src/main/reso...
Date Sat, 15 Oct 2016 00:53:40 GMT
Author: seanfinan
Date: Sat Oct 15 00:53:39 2016
New Revision: 1765001

URL: http://svn.apache.org/viewvc?rev=1765001&view=rev
Log:
FilesInDirectoryCollectionReader now uses FileLocator to access resources in source
Adding Example that reads files from a directory using PipelineBuilder
moved ctakes-examples/data/ to a ctakes-examples-res module
Added all other sample notes in ctakes project to the ctakes-examples-res module
   TODO refactor all test and sample code in ctakes to use ctakes-examples-res sample notes

Added:
    ctakes/trunk/ctakes-examples-res/
    ctakes/trunk/ctakes-examples-res/src/
    ctakes/trunk/ctakes-examples-res/src/main/
    ctakes/trunk/ctakes-examples-res/src/main/resources/
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/SampleInputRadiologyNotes.txt
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/testpatient_cn_1.xml
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/testpatient_cn_2.xml
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/claudication
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/dr_nutritious_1.txt
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/dr_nutritious_2.txt
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/edge_cases_plaintext_1.txt
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/OneMistyMoistyMorning.txt
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/README
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/pain_no_swelling.txt
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/right_knee_arthroscopy
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/GenSurg_UmbilicalHernia_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_Gen_Abscess_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_HysterectomyAndBSO_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_IUD_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_LaborProgressNote_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_MVAPrego_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_PROMCheck_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_Dysphagia_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_FebrileSez_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_RoutBirthNote_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_AAA_Leak_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_FollowUp_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_PVD_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-AAA_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT_1.rtf
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/shark_bite.txt
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_current.txt
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_past_smoker.txt
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_unknown.txt
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc2_07543210_sample_current.txt
    ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc2_07543210_sample_past_smoker.txt
    ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/DirNotesBuildPipeRunner.java
Removed:
    ctakes/trunk/ctakes-examples/data/
Modified:
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java
    ctakes/trunk/ctakes-examples/pom.xml
    ctakes/trunk/pom.xml

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java?rev=1765001&r1=1765000&r2=1765001&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java Sat Oct 15 00:53:39 2016
@@ -39,28 +39,23 @@ package org.apache.ctakes.core.cr;
  * gather files in the directory from sub directories.    
  */
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.util.ArrayList;
-import java.util.List;
-
+import org.apache.ctakes.core.resource.FileLocator;
+import org.apache.ctakes.typesystem.type.structured.DocumentID;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.CASException;
 import org.apache.uima.collection.CollectionException;
 import org.apache.uima.collection.CollectionReader_ImplBase;
 import org.apache.uima.jcas.JCas;
-//import org.apache.uima.jcas.tcas.DocumentAnnotation;
 import org.apache.uima.resource.ResourceConfigurationException;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.util.Progress;
 import org.apache.uima.util.ProgressImpl;
 
-import org.apache.ctakes.typesystem.type.structured.DocumentID;
+import java.io.*;
+import java.util.ArrayList;
+import java.util.List;
+
+//import org.apache.uima.jcas.tcas.DocumentAnnotation;
 
 public class FilesInDirectoryCollectionReader extends CollectionReader_ImplBase 
 {
@@ -107,11 +102,20 @@ public class FilesInDirectoryCollectionR
 	  /**
 	   * @see org.apache.uima.collection.CollectionReader_ImplBase#initialize()
 	   */
+	  @Override
 	public void initialize() throws ResourceInitializationException
 	{
-	    File directory = new File((String)getConfigParameterValue(PARAM_INPUTDIR));
-	    iv_encoding = (String)getConfigParameterValue(PARAM_ENCODING);
-	    iv_language = (String)getConfigParameterValue(PARAM_LANGUAGE);
+		final String inputDirPath = (String)getConfigParameterValue( PARAM_INPUTDIR );
+		File directory;
+		try {
+			directory = FileLocator.locateFile( inputDirPath );
+		} catch ( IOException ioE ) {
+			throw new ResourceInitializationException(
+					ResourceConfigurationException.DIRECTORY_NOT_FOUND,
+					new Object[] { PARAM_INPUTDIR, getMetaData().getName(), inputDirPath } );
+		}
+		iv_encoding = (String)getConfigParameterValue( PARAM_ENCODING );
+		iv_language = (String)getConfigParameterValue(PARAM_LANGUAGE);
 	    iv_extensions = (String[]) getConfigParameterValue(PARAM_EXTENSIONS);
 	    
 	    iv_currentIndex = 0;

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/SampleInputRadiologyNotes.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/SampleInputRadiologyNotes.txt?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/SampleInputRadiologyNotes.txt (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/SampleInputRadiologyNotes.txt Sat Oct 15 00:53:39 2016
@@ -0,0 +1,7 @@
+CLINIC`rimsdate`rimstime`resultno`subtype`accesion`lastname`birth_dt`gender`status`secure`testcode`testdesc`doctor`COMMENTS
+54321`02/20/1999`13:21:00`14`GENRAD`987654-3`SMITH`04/03/1916`F`F`N`70955-RRIMS`CT ANGIO ABD W/WO CST ADD SECT`DAVIS, WILLIAM R`20Feb1999 1:21PM CT ABDOMEN w & PELVIS w Indications: ct abd/pel - hernia ventral nos;USE IV CON ORIGINAL REPORT - 10 Aug 2009 3:15PM ROMAYO CT abdomen and pelvis with IV contrast. Comparison with prior MR angiography dated 4-2-04. Again seen is a large ventral hernia containing multiple nonobstructed loops of small bowel and ascending colon. No evidence of vascular compromise within this hernial sac. PO changes of aortobifemoral graft with occluded right limb of the graft just below the bifurcation. Patent femoral crossover graft. Possible diffuse fatty infiltration of the liver. Severe atrophy of the left kidney. The left renal artery is not well delineated and may be occluded. Small scarring in the lower right kidney. Low-lying urinary bladder with a possible small cystocele. Sigmoid diverticulosis. Vascular calcifications. Degenerative changes of the sp
 ine, symphysis pubis, and both SI and hip joints. Minimal atelectasis or fibrosis in the lung bases. Remainder of the study is unremarkable.. W. R. Davis MD 5-4321
+54321`02/20/1999`11:20:00`13`GENRAD`987654-4`SMITH`04/03/1916`F`F`N`07552-RRIMS`US Lower Extrem Art-Graft Cmpl`DAVIS, WILLIAM R`20Feb1999 11:20AM US Lower Extrem Art-Graft Cmpl ASO. Patent left femoral-popliteal  bypass. Diffuse tibial artery disease with posterior tibial occlusion. The anterior tibial is patent into the dorsalis pedis and the peroneal artery contributes to the plantar arch via a patent calcaneal branch. Right hypogastric artery stenosis. W. R. Davis MD 5-4321
+54321`02/20/2000`17:15:00`12`CT`876543-2`SMITH`04/03/1916`F`F`N`73200-RRIMS`CT EXT UPPER wo`DAVIS, WILLIAM R`20Feb2000 5:15PM Exam: CT RECONSTRUCTION 20Feb2000 3:17PM Exam: L CT EXT LOWER w Indications: le - L femur pain, r/o^osteomyelitis vs tumor ORIGINAL REPORT - 17 Apr 2006 2:31PM SMH CT left femur with IV contrast. No comparison exam. Along the mid left femoral diaphysis there is an aggressive, malignant appearing process involving the lateral cortex. Adjacent cortical scalloping is present. Codman's triangle's are seen at either end of the lesion consistent with aggressive periosteal reaction. The area of cortical scalloping measures 4.5 cm in length. There is some probable hazy mineral content within the peripheral lucent area suggesting that this is a malignant surface Osteogenic sarcoma. The other consideration is a periosteal Ewing's sarcoma. No associated soft tissue mass or fluid collections. Recommend further evaluation with MRI to evaluate for left femoral bone marrow 
 involvement. Exam was discussed with Dr .W. R. Davis MD 5-4321
+12345`02/20/1999`13:21:00`14`GENRAD`987654-3`SMITH`04/03/1916`F`F`N`07075-RRIMS`Tibia Fibula 2vw AP/Lat`DAVIS, WILLIAM R`20Feb1999 1:21PM Exam: R Tibia Fibula 2vw AP/Lat Indications: Exposed tibia;R/O osteo;S/p BKA ORIGINAL REPORT - 02 Feb 1999 1:21PM ROMAYO Amputation through the proximal shafts of the right tibia and fibula. Ulceration of soft tissues distally. No radiographic evidence of osteomyelitis. The right popliteal artery is largely obscured by metallic artifact from a right TKA. No radiographic evidence of loosening. Extensive arterial calcification. Cast obscures detail. W. R. Davis MD 5-4321
+12345`02/20/1999`11:20:00`13`GENRAD`987654-4`SMITH`04/03/1916`F`F`N`07552-RRIMS`US Lower Extrem Art-Graft Cmpl`DAVIS, WILLIAM R`20Feb1999 11:20AM Exam: Both popliteal arteries are patent with normal flow. W. R. Davis MD 5-4321
+12345`02/20/2000`17:15:00`12`CT`876543-2`SMITH`04/03/1916`F`F`N`73200-RRIMS`CT EXT UPPER wo`DAVIS, WILLIAM R`20Feb2000 5:15PM Exam: CT RECONSTRUCTION 20Feb2000 3:17PM Exam: CT EXT UPPER W/O CONTRAST Indications: Indications: Left shoulder fracture 02/20/2001 3:55PM SMH (2B-3495) CT of the left shoulder including oblique sagittal and oblique coronal reformats demonstrates a slightly comminuted fracture of the surgical neck of the proximal left humerus with anterior and proximal displacement and posterior angulation of the distal fragment. The fracture extends proximally into the greater humeral tuberosity and, to a lesser degree, the inferior aspect of the lesser tuberosity. The articular surface of the humeral head is intact and glenohumeral alignment maintained. W. R. Davis MD 5-4321
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/testpatient_cn_1.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/testpatient_cn_1.xml?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/testpatient_cn_1.xml (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/testpatient_cn_1.xml Sat Oct 15 00:53:39 2016
@@ -0,0 +1,330 @@
+<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE levelone SYSTEM "NotesIIST_RTF.DTD" [<!ENTITY deg '&#x00B0;'><!ENTITY sup2 '&#x00B2;'><!ENTITY micro '&#x00B5;'>]>
+<levelone>
+   <clinical_document_header>
+      <id EX="###DOC_ID###" RT="2.16.840.1.113883.3.2.1.1"/>
+      <set_id EX="###SET_ID###" RT="2.16.840.1.113883.3.2.1.2"/>
+      <version_nbr V="###V_NBR###"/>
+      <document_type_cd V="687" S="2.16.840.1.113883.3.2.1.3" DN="Nutrition Consult"/>
+      <origination_dttm V="20030822T131513"/>
+      <confidentiality_cd V="0" S="2.16.840.1.113883.3.2.1.4"/>
+      <patient_encounter>
+         <practice_setting_cd V="4284" S="2.16.840.1.113883.3.2.1.7" DN="Nutr Clinic"/>
+         <encounter_tmr V="20030822"/>
+         <service_location>
+            <id EX="TBD" RT="2.16.840.1.113883.3.2.1.8"/>
+         </service_location>
+         <facility>
+            <organization>
+               <organization.nm V="MCR"/>
+            </organization>
+         </facility>
+      </patient_encounter>
+      <legal_authenticator>
+         <legal_authenticator.type_cd V="SPV"/>
+         <participation_tmr V=""/>
+         <signature_cd V="S"/>
+         <person>
+            <id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/>
+            <person_name>
+               <nm>
+                  <GIV V="Julie"/>
+                  <MID V="A"/>
+                  <FAM V="Tester"/>
+                  <PFX V=""/>
+                  <SFX V="RD"/>
+               </nm>
+               <person_name.type_cd V="S"/>
+            </person_name>
+         </person>
+      </legal_authenticator>
+      <originator>
+         <originator.type_cd V="AUT"/>
+         <participation_tmr V="20030822T131513"/>
+         <person>
+            <id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/>
+            <person_name>
+               <nm>
+                  <GIV V="Julie"/>
+                  <MID V="A."/>
+                  <FAM V="Tester"/>
+                  <PFX V=""/>
+                  <SFX V="RD"/>
+               </nm>
+               <person_name.type_cd V="L"/>
+            </person_name>
+            <telecom V="5-5555" USE="PG"/>
+         </person>
+      </originator>
+      <originating_organization>
+         <originating_organization.type_cd V="CST"/>
+         <organization>
+            <id EX="TBD" RT="2.16.840.1.113883.3.2.1.10"/>
+            <organization.nm V="Originating Organization - Coding TBD"/>
+         </organization>
+      </originating_organization>
+      <transcriptionist>
+         <transcriptionist.type_cd V="ENT"/>
+         <participation_tmr V="20030822T131513"/>
+         <person>
+            <id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/>
+            <person_name>
+               <nm>
+                  <GIV V="Julie"/>
+                  <MID V="A."/>
+                  <FAM V="Tester"/>
+               </nm>
+               <person_name.type_cd V="L"/>
+            </person_name>
+         </person>
+      </transcriptionist>
+      <provider>
+         <provider.type_cd V="CON"/>
+         <participation_tmr V="20030822T131513"/>
+         <person>
+            <id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/>
+            <person_name>
+               <nm>
+                  <GIV V="Julie"/>
+                  <MID V="A."/>
+                  <FAM V="Tester"/>
+                  <PFX V=""/>
+                  <SFX V="RD"/>
+               </nm>
+               <person_name.type_cd V="L"/>
+            </person_name>
+            <telecom V="5-5555" USE="PG"/>
+         </person>
+      </provider>
+      <patient>
+         <patient.type_cd V="PATSBJ"/>
+         <person>
+            <id EX="3-303-925" RT="2.16.840.1.113883.3.2.1.1"/>
+            <person_name>
+               <nm>
+                  <GIV V="Terri"/>
+                  <MID V="A."/>
+                  <FAM V="Testing"/>
+                  <PFX V="Judge"/>
+                  <SFX V="Jr.,D.D.S."/>
+               </nm>
+               <person_name.type_cd V="L"/>
+            </person_name>
+            <addr>
+               <LIT V="100 Quality Control Avenue"/>
+               <CTY V="Rochester"/>
+               <STA V="MN"/>
+               <ZIP V="55905"/>
+               <CNT V="US"/>
+            </addr>
+         </person>
+         <is_known_by>
+            <id EX="TBD" RT="2.16.840.1.113883.3.2.2.1"/>
+            <is_known_to>
+               <id EX="TBD" RT="2.16.840.1.113883.3.2.1.10"/>
+            </is_known_to>
+         </is_known_by>
+         <birth_dttm V="19341123"/>
+         <administrative_gender_cd V="F" S="2.16.840.1.113883.3.2.2.2"/>
+      </patient>
+      <status_cd V="TBD" S="2.16.840.1.113883.3.2.1.16"/>
+      <cn1_admin_data>
+         <cn1_status_cd V="Fnl" S="2.16.840.1.113883.3.2.3.1"/>
+         <cn1_service_cd V="MNT" S="2.16.840.1.113883.3.2.3.2"/>
+         <cn1_event_cd V="CON" S="2.16.840.1.113883.3.2.3.3"/>
+         <cn1_document_id EX="000000000" RT="2.16.840.1.113883.3.2.3.4"/>
+         <cn1_revision_nbr V="1"/>
+         <cn1_site_cd V="RCH" S="2.16.840.1.113883.3.2.3.10"/>
+      </cn1_admin_data>
+      <document_title V="Document Service Name - Coding TBD" S="2.16.840.1.113883.3.2.1.17"/>
+   </clinical_document_header>
+   <body>
+      <section>
+         <caption><caption_cd V="20100" DN="Revision History" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Revision History
+         </caption>
+      </section>
+      <section>
+         <caption><caption_cd V="20112" DN="I/R/P" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Impression / Report / Plan
+         </caption>
+         <table>
+            <caption>
+               <caption_cd V="20003" DN="I/R/P" S="2.16.840.1.113883.3.1.21" SV="1.0"/>
+            </caption>
+            <tr>
+               <th>Problem</th>
+               <th>Plan</th>
+            </tr>
+         </table>
+      </section>
+      <section>
+         <caption><caption_cd V="20113" DN="Diagnoses" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Diagnosis
+         </caption>
+         <table>
+            <caption>
+               <caption_cd V="20003" DN="Diagnoses" S="2.16.840.1.113883.3.1.21" SV="1.0"/>
+            </caption>
+            <tr>
+               <th>Problem</th>
+               <th>Diagnosis</th>
+            </tr>
+         </table>
+      </section>
+      <section>
+         <caption><caption_cd V="20101" DN="Ref" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Referral Source
+         </caption>
+         <paragraph>
+            <content>Dr. Nutritious</content>
+         </paragraph>
+      </section>
+      <section>
+         <caption><caption_cd V="20102" DN="CC" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Chief Complaint/Reason for Visit
+         </caption>
+         <paragraph>
+            <content>Medical Nutrition Therapy for Hyperlipidemia</content>
+         </paragraph>
+      </section>
+      <section>
+         <caption><caption_cd V="20103" DN="HPI" S="2.16.840.1.113883.3.1.21" SV="1.0"/>History of Present Illness
+         </caption>
+         <table>
+            <caption>
+               <caption_cd V="20003" DN="HPI" S="2.16.840.1.113883.3.1.21" SV="1.0"/>
+            </caption>
+            <tr>
+               <th>Problem</th>
+               <th>History</th>
+            </tr>
+            <tr>
+               <td/>
+               <td>
+                  <paragraph>
+                     <content>Referral from: Julie Tester, RD, LD, CNSD</content>
+                  </paragraph>
+               </td>
+            </tr>
+            <tr>
+               <td/>
+               <td>
+                  <paragraph>
+                     <content>Phone contact: (555) 555-1212</content>
+                  </paragraph>
+               </td>
+            </tr>
+            <tr>
+               <td/>
+               <td>
+                  <paragraph>
+                     <content>Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2</content>
+                  </paragraph>
+               </td>
+            </tr>
+            <tr>
+               <td/>
+               <td>
+                  <paragraph>
+                     <content>Diet: General</content>
+                  </paragraph>
+               </td>
+            </tr>
+            <tr>
+               <td/>
+               <td>
+                  <paragraph>
+                     <content>Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.</content>
+                  </paragraph>
+               </td>
+            </tr>
+            <tr>
+               <td/>
+               <td>
+                  <paragraph>
+                     <content>Daily Protein needs: 40 grams, assessed as 1.0 g/kg.</content>
+                  </paragraph>
+               </td>
+            </tr>
+            <tr>
+               <td/>
+               <td>
+                  <paragraph>
+                     <content>Pt has been on a 3 day calorie count and has had an average intake of 1100 calories. She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain. She agrees with the plan and has my number for further assessment. May want a Resting Metabolic Rate as well. She takes an aspirin a day for knee pain.</content>
+                  </paragraph>
+               </td>
+            </tr>
+         </table>
+         <table>
+            <caption>
+               <caption_cd V="20004" DN="MC985" S="2.16.840.1.113883.3.1.21" SV="1.0"/>
+            </caption>
+            <tr>
+               <th><caption_cd V="30001" DN="PFH Date" S="2.16.840.1.113883.3.1.22" SV="1.0"/>PFH Date
+               </th>
+               <th><caption_cd V="30002" DN="CVI Page#" S="2.16.840.1.113883.3.1.22" SV="1.0"/>CVI Page#
+               </th>
+               <th><caption_cd V="30003" DN="CVI Date" S="2.16.840.1.113883.3.1.22" SV="1.0"/>CVI Date
+               </th>
+            </tr>
+            <tr>
+               <td></td>
+               <td></td>
+               <td></td>
+            </tr>
+         </table>
+      </section>
+      <section>
+         <caption>
+            <caption_cd V="20107" DN="Med/Surg Hx" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Past Medical/Surgical History
+         </caption>
+      </section>
+      <section>
+         <caption><caption_cd V="20105" DN="Allerg" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Allergies
+         </caption>
+      </section>
+      <section>
+         <caption><caption_cd V="20108" DN="Soc Hist" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Social History
+         </caption>
+      </section>
+      <section>
+         <caption><caption_cd V="20109" DN="Fam Hist" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Family History
+         </caption>
+      </section>
+      <section>
+         <caption><caption_cd V="20104" DN="Meds" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Current Medications
+         </caption>
+      </section>
+      <section>
+         <caption><caption_cd V="20106" DN="Sys Rev" S="2.16.840.1.113883.3.1.21" SV="1.0"/>System Review
+         </caption>
+      </section>
+      <section>
+         <caption><caption_cd V="20115" DN="Spec Instr" S=".16.840.1.113883.3.1.21" SV="1.0"/>Special Instructions
+         </caption>
+      </section>
+      <section>
+         <caption><caption_cd V="20114" DN="Administrative" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Administrative
+         </caption>
+         <table>
+            <caption>
+               <caption_cd V="20005" DN="Billing" S="2.16.840.1.113883.3.1.21" SV="1.0"/>
+            </caption>
+            <tr>
+               <th>Billing</th>
+               <th>Value</th>
+            </tr>
+            <tr>
+               <th><caption_cd V="30004" DN="Margin Code" S="2.16.840.1.113883.3.1.22" SV="1.0"/>Margin Code
+               </th>
+               <td></td>
+            </tr>
+            <tr>
+               <th><caption_cd V="30005" DN="Total Time" S="2.16.840.1.113883.3.1.22" SV="1.0"/>Total Time
+               </th>
+               <td></td>
+            </tr>
+            <tr>
+               <th><caption_cd V="30006" DN="Counseling Time" S="2.16.840.1.113883.3.1.22" SV="1.0"/>Counseling Time
+               </th>
+               <td></td>
+            </tr>
+         </table>
+      </section>
+   </body>
+</levelone>
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/testpatient_cn_2.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/testpatient_cn_2.xml?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/testpatient_cn_2.xml (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/testpatient_cn_2.xml Sat Oct 15 00:53:39 2016
@@ -0,0 +1,254 @@
+<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE levelone SYSTEM "NotesIIST_RTF.DTD" [<!ENTITY deg '&#x00B0;'><!ENTITY sup2 '&#x00B2;'><!ENTITY micro '&#x00B5;'>]>
+<levelone>
+   <clinical_document_header>
+      <id EX="###DOC_ID###" RT="2.16.840.1.113883.3.2.1.1"/>
+      <set_id EX="###SET_ID###" RT="2.16.840.1.113883.3.2.1.2"/>
+      <version_nbr V="###V_NBR###"/>
+      <document_type_cd V="687" S="2.16.840.1.113883.3.2.1.3" DN="Nutrition Consult"/>
+      <origination_dttm V="20030822T131513"/>
+      <patient_encounter>
+         <practice_setting_cd V="4284" S="2.16.840.1.113883.3.2.1.7" DN="Nutr Clinic"/>
+         <encounter_tmr V="20030822"/>
+         <service_location>
+            <id EX="TBD" RT="2.16.840.1.113883.3.2.1.8"/>
+         </service_location>
+         <facility>
+            <organization>
+               <organization.nm V="MCR"/>
+            </organization>
+         </facility>
+      </patient_encounter>
+      <legal_authenticator>
+         <legal_authenticator.type_cd V="SPV"/>
+         <participation_tmr V=""/>
+         <signature_cd V="S"/>
+         <person>
+            <id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/>
+            <person_name>
+               <nm>
+                  <GIV V="Julie"/>
+                  <MID V="A"/>
+                  <FAM V="Tester"/>
+                  <PFX V=""/>
+                  <SFX V="RD"/>
+               </nm>
+               <person_name.type_cd V="S"/>
+            </person_name>
+         </person>
+      </legal_authenticator>
+      <originator>
+         <originator.type_cd V="AUT"/>
+         <participation_tmr V="20030822T131513"/>
+         <person>
+            <id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/>
+            <person_name>
+               <nm>
+                  <GIV V="Julie"/>
+                  <MID V="A."/>
+                  <FAM V="Tester"/>
+                  <PFX V=""/>
+                  <SFX V="RD"/>
+               </nm>
+               <person_name.type_cd V="L"/>
+            </person_name>
+            <telecom V="5-5555" USE="PG"/>
+         </person>
+      </originator>
+      <originating_organization>
+         <originating_organization.type_cd V="CST"/>
+         <organization>
+            <id EX="TBD" RT="2.16.840.1.113883.3.2.1.10"/>
+            <organization.nm V="Originating Organization - Coding TBD"/>
+         </organization>
+      </originating_organization>
+      <transcriptionist>
+         <transcriptionist.type_cd V="ENT"/>
+         <participation_tmr V="20030822T131513"/>
+         <person>
+            <id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/>
+            <person_name>
+               <nm>
+                  <GIV V="Julie"/>
+                  <MID V="A."/>
+                  <FAM V="Tester"/>
+               </nm>
+               <person_name.type_cd V="L"/>
+            </person_name>
+         </person>
+      </transcriptionist>
+      <provider>
+         <provider.type_cd V="CON"/>
+         <participation_tmr V="20030822T131513"/>
+         <person>
+            <id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/>
+            <person_name>
+               <nm>
+                  <GIV V="Julie"/>
+                  <MID V="A."/>
+                  <FAM V="Tester"/>
+                  <PFX V=""/>
+                  <SFX V="RD"/>
+               </nm>
+               <person_name.type_cd V="L"/>
+            </person_name>
+            <telecom V="5-5555" USE="PG"/>
+         </person>
+      </provider>
+      <patient>
+         <patient.type_cd V="PATSBJ"/>
+         <person>
+            <id EX="3-303-925" RT="2.16.840.1.113883.3.2.1.1"/>
+            <person_name>
+               <nm>
+                  <GIV V="Terri"/>
+                  <MID V="A."/>
+                  <FAM V="Testing"/>
+                  <PFX V="Judge"/>
+                  <SFX V="Jr.,D.D.S."/>
+               </nm>
+               <person_name.type_cd V="L"/>
+            </person_name>
+            <addr>
+               <LIT V="100 Quality Control Avenue"/>
+               <CTY V="Rochester"/>
+               <STA V="MN"/>
+               <ZIP V="55905"/>
+               <CNT V="US"/>
+            </addr>
+         </person>
+         <is_known_by>
+            <id EX="TBD" RT="2.16.840.1.113883.3.2.2.1"/>
+            <is_known_to>
+               <id EX="TBD" RT="2.16.840.1.113883.3.2.1.10"/>
+            </is_known_to>
+         </is_known_by>
+         <birth_dttm V="19341123"/>
+         <administrative_gender_cd V="F" S="2.16.840.1.113883.3.2.2.2"/>
+      </patient>
+      <status_cd V="TBD" S="2.16.840.1.113883.3.2.1.16"/>
+      <cn1_admin_data>
+         <cn1_status_cd V="Fnl" S="2.16.840.1.113883.3.2.3.1"/>
+         <cn1_service_cd V="MNT" S="2.16.840.1.113883.3.2.3.2"/>
+         <cn1_event_cd V="CON" S="2.16.840.1.113883.3.2.3.3"/>
+         <cn1_document_id EX="000000000" RT="2.16.840.1.113883.3.2.3.4"/>
+         <cn1_revision_nbr V="1"/>
+         <cn1_site_cd V="RCH" S="2.16.840.1.113883.3.2.3.10"/>
+      </cn1_admin_data>
+      <document_title V="Document Service Name - Coding TBD" S="2.16.840.1.113883.3.2.1.17"/>
+   </clinical_document_header>
+   <body>
+      <section>
+         <caption><caption_cd V="20100" DN="Revision History" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Revision History
+         </caption>
+      </section>
+      <section>
+         <caption><caption_cd V="20112" DN="I/R/P" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Impression / Report / Plan
+         </caption>
+         <table>
+            <caption>
+               <caption_cd V="20003" DN="I/R/P" S="2.16.840.1.113883.3.1.21" SV="1.0"/>
+            </caption>
+            <tr>
+               <th>Problem</th>
+               <th>Plan</th>
+            </tr>
+         </table>
+      </section>
+      <section>
+         <caption><caption_cd V="20113" DN="Diagnoses" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Diagnosis
+         </caption>
+         <table>
+            <caption>
+               <caption_cd V="20003" DN="Diagnoses" S="2.16.840.1.113883.3.1.21" SV="1.0"/>
+            </caption>
+            <tr>
+               <th>Problem</th>
+               <th>Diagnosis</th>
+            </tr>
+         </table>
+      </section>
+      <section>
+         <caption><caption_cd V="20101" DN="Ref" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Referral Source
+         </caption>
+         <paragraph>
+            <content>Dr. Nutritious</content>
+         </paragraph>
+      </section>
+      <section>
+         <caption><caption_cd V="20102" DN="CC" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Chief Complaint/Reason for Visit
+         </caption>
+         <paragraph>
+            <content>Medical Nutrition Therapy for Hyperlipidemia</content>
+         </paragraph>
+      </section>
+      <section>
+         <caption><caption_cd V="20103" DN="HPI" S="2.16.840.1.113883.3.1.21" SV="1.0"/>History of Present Illness
+         </caption>
+         <table>
+            <caption>
+               <caption_cd V="20003" DN="HPI" S="2.16.840.1.113883.3.1.21" SV="1.0"/>
+            </caption>
+            <tr>
+               <th>Problem</th>
+               <th>History</th>
+            </tr>
+            <tr>
+               <td/>
+               <td>
+                  <paragraph>
+                     <content>Significant for her father, who died at 50 years from colon cancer.</content>
+                  </paragraph>
+               </td>
+            </tr>
+            <tr>
+               <td/>
+               <td>
+                  <paragraph>
+                     <content>Phone contact: (555) 555-1212</content>
+                  </paragraph>
+               </td>
+            </tr>
+            <tr>
+               <td/>
+               <td>
+                  <paragraph>
+                     <content>Height: 144 cm Current Weight: 45 kg</content>
+                  </paragraph>
+               </td>
+            </tr>
+            <tr>
+               <td/>
+               <td>
+                  <paragraph>
+                     <content>Diet: General</content>
+                  </paragraph>
+               </td>
+            </tr>
+            <tr>
+               <td/>
+               <td>
+                  <paragraph>
+                     <content>Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.</content>
+                  </paragraph>
+               </td>
+            </tr>
+            <tr>
+               <td/>
+               <td>
+                  <paragraph>
+                     <content>Daily Protein needs: 40 grams, assessed as 1.0 g/kg.</content>
+                  </paragraph>
+               </td>
+            </tr>
+            <tr>
+               <td/>
+               <td>
+                  <paragraph>
+                     <content>Colonoscopy. No pain or discomfort reported.</content>
+                  </paragraph>
+               </td>
+            </tr>
+         </table>
+      </section>
+   </body>
+</levelone>
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/claudication
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/claudication?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/claudication (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/claudication Sat Oct 15 00:53:39 2016
@@ -0,0 +1,7 @@
+IMPRESSION/REPORT/PLAN
+The patient has very typical history for claudication. Yet the patient does not have any significant bruit at the pelvic area, abdominal area.
+
+Aspirin 200-mg once-a-day.
+Ibuprofen increased from 200 mg to 300 mg p.o. twice a day.
+Aspirin 80 mg.
+acetaminophen discontinued.

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/dr_nutritious_1.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/dr_nutritious_1.txt?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/dr_nutritious_1.txt (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/dr_nutritious_1.txt Sat Oct 15 00:53:39 2016
@@ -0,0 +1,12 @@
+
+Dr. Nutritious
+
+Medical Nutrition Therapy for Hyperlipidemia
+
+Referral from: Julie Tester, RD, LD, CNSD
+Phone contact: (555) 555-1212
+Height: 144 cm   Current Weight: 45 kg   Date of current weight: 02-29-2001   Admit Weight:  53 kg   BMI: 18 kg/m2
+Diet: General
+Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.
+Daily Protein needs: 40 grams,  assessed as 1.0 g/kg.
+Pt has been on a 3-day calorie count and has had an average intake of 1100 calories.  She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.  She agrees with the plan and has my number for further assessment. May want a Resting Metabolic Rate as well. She takes an aspirin a day for knee pain.

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/dr_nutritious_2.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/dr_nutritious_2.txt?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/dr_nutritious_2.txt (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/dr_nutritious_2.txt Sat Oct 15 00:53:39 2016
@@ -0,0 +1,12 @@
+
+Dr. Nutritious
+
+Medical Nutrition Therapy for Hyperlipidemia
+
+Significant for her father, who died at 50 years from colon cancer.
+Phone contact: (555) 555-1212
+Height: 144 cm   Current Weight: 45 kg
+Diet: General
+Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.
+Daily Protein needs: 40 grams,  assessed as 1.0 g/kg.
+Colonoscopy. No pain or discomfort reported.

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/edge_cases_plaintext_1.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/edge_cases_plaintext_1.txt?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/edge_cases_plaintext_1.txt (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/edge_cases_plaintext_1.txt Sat Oct 15 00:53:39 2016
@@ -0,0 +1,2 @@
+patient complained that the n'tion didn't make sense.  This is a test of an edge case in contraction in the tokezier.
+aspirin decreased from 2:00 PM.  This used to cause the drug ner to go into an infinte loop.
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/OneMistyMoistyMorning.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/OneMistyMoistyMorning.txt?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/OneMistyMoistyMorning.txt (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/OneMistyMoistyMorning.txt Sat Oct 15 00:53:39 2016
@@ -0,0 +1,6 @@
+One misty, moisty morning,
+When cloudy was the weather,
+I chanced to meet an old man clothed all in leather.
+He began to compliment, and I began to grin,
+How do you do, and how do you do?
+And how do you do again?
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/README
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/README?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/README (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/README Sat Oct 15 00:53:39 2016
@@ -0,0 +1,3 @@
+All of the files in this directory were obtained from Project GutenBerg at:
+
+http://www.gutenberg.org/files/24623/24623-h/24623-h.htm

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/pain_no_swelling.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/pain_no_swelling.txt?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/pain_no_swelling.txt (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/pain_no_swelling.txt Sat Oct 15 00:53:39 2016
@@ -0,0 +1,4 @@
+
+The patient reported pain in her upper arm.
+No swelling.
+Aspirin 325 mg.

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/right_knee_arthroscopy
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/right_knee_arthroscopy?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/right_knee_arthroscopy (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/right_knee_arthroscopy Sat Oct 15 00:53:39 2016
@@ -0,0 +1,2 @@
+S/P right knee arthroscopy.
+Knee x-ray.  Patient denies knee pain.

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/GenSurg_UmbilicalHernia_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/GenSurg_UmbilicalHernia_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/GenSurg_UmbilicalHernia_1.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/GenSurg_UmbilicalHernia_1.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,36 @@
+{\rtf1\ansi\ansicpg1252\cocoartf1138\cocoasubrtf510
+{\fonttbl\f0\fswiss\fcharset0 ArialMT;}
+{\colortbl;\red255\green255\blue255;}
+\margl1440\margr1440\vieww10800\viewh8400\viewkind0
+\deftab720
+\pard\pardeftab720
+
+\f0\fs24 \cf0 Case description for C-Takes documenting:\
+Setting: Outpatient.\
+Specialty: General Surgery.\'a0\
+Note detail level (1-5): 3.\
+Level of abbreviation (Low/Medium/High): Medium.\'a0\
+\
+CC/HPI: Mrs. X is a 66 yo caucasian woman w/ a known hist of umbilical hernia who presents to the clinic for f/u of a suspected umbilical hernia s/p panni. The panni was performed on 2 Feb 2010. She presented to the clinic 3 weeks ago for 'redness' and TTP periumbilically. At that time an umbilical hernia was suspected, however the US at that time was documented as being negative. Patient was scheduled for f/u today. She describes that it feels worse after being "on her feet all day". Better or gone when she lies down. When she eats it feels like "her guts are going to pop out". It also feels like she needs to burp all the time like "she drank a soda". This is the first day she has been able to get around relatively comfortably w/o her abdominal binder. She can not eat much due to all of the above. She states that the symptoms she is experiencing are consistent with the symptioms she felt 17 years ago when she had an umbilical hernia.\'a0\
+\pard\pardeftab720\sa240
+\cf0 ROS:\'a0Denies n/v/cp/sob/f/c/ns.\'a0Reflux/burping as noted. Consistently constipated and when she bears down now\'a0 s/p panni, she can not feel herself deficate. She does have atleast one bowel a day on average. She has had bladder dysfunction for which she is seeing OBGYN, however it seems to have began before the panni.\
+\pard\pardeftab720
+\cf0 PMHx: Umbilical hernia 17 years ago, thyroid cancer, gall bladder disease, HTN.\
+\
+PSHx: Panni, Breast reduction, Cholcystectomy, partial thyroidectomy.\
+\
+Meds: Lisinopril, Mobec, Primpro, Synthroid, Prilosec, Zocar, Asp, Zirtec, Hydrochlorothyazide.\
+\
+Allergies: Sulfa.\
+\pard\pardeftab720\sa240
+\cf0 PE:\uc0\u8232 CV: No r/m/g. RRR.\u8232 Pulm: CTAB.\u8232 Abd: Inspection of the abdomen revealed NBS. Periumbilical erythema with TTP was appreciated. Bulging at umbilicis on valsalva.\
+\pard\pardeftab720
+\cf0 Labs/Ancillary studies:\'a0\
+US: Revealed no disruption of the abdominal fascia while standing or while standing w/ valsalva.\
+\
+A/P:\'a0\
+Umbilical hernia: Mrs. X is a 66 yo woman in no acute distress who is now s/p panni w/ a known history of umbilical hernia 17 years ago with s/s c/w with an umbilical hernia but negative US.\'a0\
+- Check creatinine with BMP.\
+- Order CT with PO/IV contrast.\
+- Schedule f/u after results.\
+}
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_Gen_Abscess_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_Gen_Abscess_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_Gen_Abscess_1.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_Gen_Abscess_1.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,30 @@
+Case description for C-Takes documenting:
+Setting: Outpatient.
+Specialty: Ob/Gyn. 
+Note detail level (1-5): 4.
+Level of abbreviation (Low/Medium/High): Medium.
+
+Mrs. X is a 45 y/o G2P2 with LMP of 6Feb10 using BTL for contraception. She presents to the clinic for f/u of labial and perianal abscess for which she was seen last week. Patient was recently traveling in Brazil. Patient arrived in a hotel in Rio on 10Jan which she described as Òincredibly filthyÓ. Within 2 weeks of arriving she developed an acute throat irritation ("Laryngitis" in her words) that persisted apprx 2 weeks during which time she felt feverish and short of breath with severe general malaise. Appx one month after arriving she noticed a cyst on her labia majora as well as around her anus and enlargement of the inguinal lymph nodes. When asked to hypothesize on what may have caused the infection, she feels it may have been the toilet seat in the hotel room. Cysts came and went as she popped them, some as large as "marbles" and one the size of a "golf ball". Patient saw provider in Rio who performed I&D of labial and perianal abscesses. The primary abscess was drained wi
 th approx 4cc of fluid being removed and she returned home to Austin. Today she states that she continues to feel some swelling in the area but it has overall improved. She continues to feel malaise and "not herself". She is currently in 3/10 pain and states that, currently, most of lesions are healed after a course of "something" that they gave her in Rio. Also of note and concern to the patient is a new onset rash in the right axilla as well as medial thigh. She denies any significant medical history or any similar occurences in the past. She reports that she is in a monogamous relationship but is amenable to STI testing. Denies sick contacts. Denies CP, SOB, VB/Discharge, fever/nv.
+
+ROS: General malaise, otherwise unremarkable.
+PMHx: Noncontrib.
+PSHx: Breast augmentation, BTL.
+Meds: Bactrim for abscess (obtained in Rio, read from pill bottle).
+Allergies: NKDA.
+OB: TSVD x 2, uncomplicated.
+Gyn: Denies STIs and abnormal paps, BTL.
+FamHx: Noncontrib.
+
+Vit: BP 124/71 HR 70 RR 18 Tc 98.0
+PE: Reveals a thin, well developed caucasian woman of stated age in no acute distress. 
+Pelvic: Speculum exam: Two lesions on the patients right labia majora and one on the left. All three healing well at this time. No other lesions noted on the exterior. No lesions on the interior. Posterior cervix, medium sized, parous, not friable, no discharge. Palpable inguinal lymph nodes bilaterally approximately the size of large marbles, very prominent. 
+CV: No m/r/g, rrr.
+Pulm: CTAB.
+Abd: Non-distended, symettrical, flat, well toned. Not tender to palpation. Normal bowel sounds auscultated. 
+Skin: Silver dollar size erythematous lesions at approx the location of the right axilla as wel as the right medial thigh.
+
+Lab/Ancillary:
+Swabbed KOH/Wet prep, Gon/Chlam pending.
+
+A/P:
+Genital skin abscess: reveals a 45 y/o G2P2 with LMP appx 2 weeks ago using BTL for contraception with labial and perianal abscess. Abscess appears to be healing well w/o e/o further infection. Pt had concurrent inguinal lymphadenectomy, fever, chills, malaise and laryngitis and was traveling at the time. Considering these findings, will test for HIV, RPR and gc/chlamydia. Pt amenable to being tested for STIs. 1g azithromycin given prophylactic for LGV- if positive will continue with 2 additional weekly doses. Will refer to derm for eval of axillary/thigh skin lesions. Pt is to f/u in one week to review lab results. Return precautions discussed. Pt voiced understanding of plan, all questions answered.

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_HysterectomyAndBSO_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_HysterectomyAndBSO_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_HysterectomyAndBSO_1.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_HysterectomyAndBSO_1.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,28 @@
+Case description for C-Takes documenting:
+Setting: Inpatient.
+Specialty: OB/GYN. 
+Note detail level (1-5): 2.
+Level of abbreviation (Low/Medium/High): Medium.
+
+S:
+Mrs X is a 61 yo caucasian woman G2P2 now POD 1 s/p TLH/BSO/PPALND complicated by a minor bowel perforation. Procedure for Endometriod adenocarcinoma FIGO grade 1.
+Overnight: Patient denies n/v, chills/fevers/night sweats. She is not ambulating. Foley is still in. She has not passed flatus or stool. Is eating a little.
+Pain is well controlled on Ultram.
+
+O:
+Vits: HR 86 (86), BP 108/69 (132/81) Tmax 99.5 Tc 99.5 RR 18(20) Spo2 95 RA
+I: 1325 O: 2200
+CV: No r/m/g, rrr. 
+Pulm: CTAB
+Abdom: Non distended, norm bowel snds, not tender to palp. 
+Inc: Clean, intact, mildly erythematous 
+
+Labs/Anc: 13.1/13.8/218/40.7 - 138/3.5/105.2/23/9.4/0.65<134
+
+A/P:
+Mrs. X is a 62 yo POD 1 from TLH/BSO/PPALND doing well with no acute issues. 
+- Continue incentive spirometry. 
+- Continue to advance diet as tolerated. 
+- Return to home meds on discharge.
+- Continue DVT proph. until ambulating.
+- DC foley when ambulating. DC IV. Once ambulating and making urine without foley/IV, discharge home. 
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_IUD_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_IUD_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_IUD_1.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_IUD_1.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,26 @@
+Case description for C-Takes documenting:
+Setting: Outpatient.
+Specialty: OB/GYN. 
+Note detail level (1-5): 2.
+Level of abbreviation (Low/Medium/High): Medium.
+
+HPI/CC: Mrs. X is a 33yo G1P1 with a LMP of Feb 5th and a known history of PCOS who presents to the clinic today with a CC of pelvic pain, spotting, and vaginal odor.
+Patient had an Mirena IUD placed on the 6th of Feb. Since that time she has experienced cyclic suprapubic/vaginal pain that she associates with the IUD placement.
+The pain has ranged from 6-10/10. Patient has been taking Norco prescribed for chronic back pain to help "deal" with the IUD related pain.Patient reports feeling dizzy
+and lightheaded since the placement. Upon further questioning patient reports that her partner can "feel the strings poking him" during intercourse.
+However, she claims she can not locate the IUD strings on self examination.
+
+ROS: Patient denies n/v, f/ns, sob, and cp. She denies dysuria and reports normal bowel movements. 
+PMHx: PCOS, otherwise not contributory.
+SurgHx: Not contributory.
+FamHx: Not contributory.
+SocHx: Not contributory.
+Meds: Gabapentin/Norco (chronic back pain).
+
+Vits: BP 113/67, HR 59, T 98.4
+PE: Reveals a fairly fit woman of stated age in mild distress. Normal labia. No discharge on speculum exam but some blood was noted in the vault along with a faint
+unpleasant odor. 
+
+Labs/Anc: KOH Wet prep revealed multiple hyphae per hpf. Gen probe pending. 
+
+A/P: Mrs. X is a 33yo G1P1 in no acute distress. In clinic for IUD check. Found to have yeast infection incidentally on KOH wet prep. Will treat with diflucan. 

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_LaborProgressNote_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_LaborProgressNote_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_LaborProgressNote_1.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_LaborProgressNote_1.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,13 @@
+Case description for C-Takes documenting:
+Setting: Inpatient.
+Specialty: OB/GYN. 
+Note detail level (1-5): 1.
+Level of abbreviation (Low/Medium/High): Low.
+
+S: Pt is comfortable s/p epidural, rates pain as a 2/10.
+
+O: Vital signs stable, T99.0. FHR: 145 with moderate variability, pos accels, no recurrent decels. Strong contractions palpated 2/10min. RT soft. AROM, Clear fluid.
+
+A: Cat 1 tracing, labor progressing.
+
+P: Close observation of maternal fetal well being and labor progression. Re-eval in 2hrs or PRN.

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_MVAPrego_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_MVAPrego_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_MVAPrego_1.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_MVAPrego_1.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,22 @@
+Case description for C-Takes documenting:
+Setting: Outpatient.
+Specialty: OB/GYN. 
+Note detail level (1-5): 2.
+Level of abbreviation (Low/Medium/High): Medium.
+
+HPI/CC: Mrs. X is a 22 yo G1P0 at 14 and 2 in an uncomplicated pregnancy who presents to the clinic today with a CC of continued MSK of 1st-3rd metacarpophalangeal joints s/p MVA 4 weeks ago. She is currently in 4/10 pain and is wearing a brace on her right hand. It is significantly interfering with her ability to perform her work as a waitress. FHTs@154. Currently has a UTI being managed by another provider. Patient reports some nausea that she associates with the pregnancy and some SOB also, she feels, associated with the pregnancy. 
+
+ROS: Patient denies vomiting, night sweats, fever, cp, vaginal bleeding/discharge
+PMHx: Migraines. 
+SHx: Not contributory.
+FamHx:Not contributory.
+SocHx: Asked about domestic violence. Patient denies domestic violence at home.
+Meds: Fioricet for migraines. Tylenol, PNV, and an antibiotic she could not recall for a UTI diagnosed three days by another provider. 
+
+Vits: BP 121/64, HR 97, T 98.7
+PE:
+Reveals a slightly overweight healthy appearing woman of her stated age and gestation. After removing right hand brace, joints appear slightly swollen compared to the contralateral side. No erythema, heat. Slightly decreased hand strength/ROM. No tingling, numbness.
+
+Labs/Anc: FHT 154. Radiograph done of wrist at time of accident - does not fully visualize the affected area. From what can be seen: no fractures.
+
+A/P: Mrs. X is a 22yo G1P0 at 14 and 2 with FHTs@154 s/p MVA with right hand pain. Reassure her. Give her ibuprofen and council her not to take it after 21 weeks. 

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_PROMCheck_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_PROMCheck_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_PROMCheck_1.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_PROMCheck_1.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,33 @@
+Case description for C-Takes documenting:
+Setting: Outpatient.
+Specialty: OB/GYN. 
+Note detail level (1-5): 3.
+Level of abbreviation (Low/Medium/High): Medium.
+
+Mrs. X is a 31 yo G4P3003 at 25+1 weeks who presents with a CC of leakage of fluid after urinating and while walking. Her pregnancy has been uncomplicated to date. The leakage began two days ago in the afternoon. It has continued until today, when she came in to the clinic at the urging of a friend. It is worse when she walks and after urination. The fluid appears clear on a pad. It is not copious. She thinks that it may be coming from her vagina, but she is unsure. Denies gush of fluid, VB, CTX. There is +FM.
+
+ROS: She denies urinary symptoms, cp/sob/n/v/ns/ha/changes in vision.
+GynHx: Last pap last year. No history of abnormal paps. Chlamydia in college. Three previous pregnancies resulted in uncomplicated SVDs. Pelvis proven to 6lbs 6oz. Last pregnancy complicated by GDM.
+PMHx: Pt reports congenital heart murmor.
+SurgHx: Non contrib.
+FamHx: Non contrib.
+Meds: PNV - denies any other medications.
+Allergies: NKDA
+
+Vit: Tc 97.9 BP 111/66 HR 80 RR 18 SpO2 100% 
+PE: Well appearing AA woman who appears her stated age and in no acute distress.
+CV: No m/r/g, rrr.
+Abd: Gravid abdomen consistent with gestational age. Gross fetal movement noted.
+Gyn: No leakage of urine w/ cough. Speculum exam: Diffuse vaginal sidewall tenderness, scant amount of off-white cervical discharge. No odor. No pooling in posterior fornix. Closed cervical os without friability. No blood noted in vault nor otherwise abnormal discharge.
+
+Labs/Studies:
+KOH/Wet prep showed no clue cells/spores/hyphae.
+Fern test neg. Nitrazine test neg.
+Gon/Chlamydia pending.
+US: AFI 17cm. Observed fetal cardiac activity.
+NST: reactive.
+FHR: 140s w/ pos accels. Rare variable decel. Moderate variability.
+
+A/P:
+Possible PROM: Mrs. X is a 33 yo G4P3003 at 25+1 weeks in no acute distress. No signs of PROM observed given absence of ferning, neg nitrazine test and AFI WNL. No signs/symptoms of PTL given history and tocometer. Though patient had vaginal wall tenderness on pelvic exam, KOH and wetprep unrevealing for evidence of candidal/BV infection and other suggestive symptoms absent.
+- Discussed with patient to return to triage for vaginal bleeding, s/s of PTL, developing s/s of candidal infection or other new/concerning symptoms. Otherwise to follow up for ROB care. Patient indicates understanding and agrees with this plan.

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_Dysphagia_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_Dysphagia_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_Dysphagia_1.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_Dysphagia_1.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,48 @@
+Case description for C-Takes documenting:
+Setting: Outpatient.
+Specialty: Pediatrics. 
+Note detail level (1-5): 5.
+Level of abbreviation (Low/Medium/High): Low.
+
+CC/HPI:
+Mrs X is a 13 year old female who presents to the clinic with a chief complaint of "difficulty swallowing". The onset has been gradual and over the past year. It is intermittent and associated with specific foods: chocolate and some meats, though her recollection is Òshoddy at bestÓ. She has GERD, and has since she was a baby. Her mother reports she always spit up as an infant. She knows this difficulty swallowing is different from the GERD she has experienced in the past. She takes omeprazole 20mg daily and has for years. The sensation, she reports, is a very different feeling. She further reports that she has not experienced GERD in years and that attacks of GERD do noT precede dysphagic episodes. When she points to the location that the difficulty seems to arise she indicates her midline at the level of the first intercostal space. It has recently lead to a burning (5/10 when it happens) sensation and a need to vomit. It is non-bilious vomit and looks exactly like what she just
  swallowed. There is no associated difficulty breathing. Sometimes taking a deep breath to "make more room in her chest helps" the offending food to go down. She has noted some allergic reactions that have led to lip and ÒmouthÓ swelling and have necessitated benadryl use per her mother. These have included various foods, most notably chocolate. Her dad recalls for her that it is most notably milk and milk chocolate. The picture is not entirely clear. She is unable to recall any other foods at this time, though she knows there are others. So do her parents. They cannot recall either. She denies dysphagia associated with liquids. She denies odynophagia. She denies new medications or taking any new pills. She has no other complaints today.
+
+ROS: 
+She denies any metallic taste or burning sensation in her throat. She denies waking nauseated or a chronic cough. She denies fevers, chills, nausea, or vomiting. She denies unexpected weight loss or myalgia. She denies headache. She denies chest pain, shortness of breath, or difficulty breathing. She denies diarrhea, constipation, or changes in stool.
+
+Past Medical History:
+Mrs X has a history significant for mild intermittent asthma. She has no other past medical history. 
+
+Past Surgical History:
+Mrs X has never had a surgery to include wisdom teeth. 
+
+Allergies:
+Mrs X has seasonal allergies. She denies any other allergies at this time to include penicillins or foods or latex. 
+
+Medications: 
+Mrs X is on a short acting inhaler. She takes a multivitamin. She takes the aforementioned omeprazole 20mg daily. She takes no other medications.
+
+Immunizations:
+Mrs X is up to date on all of her immunizations today.
+
+Family History:
+Her Mother and Father present with her to the clinic today. They claim to be well despite the "normal aging issues". Mom had a endometrial polyp removed recently and is a breast cancer survivor. Her father states that he has no health concerns but his wife says that he sometimes has "heart problems" but the family doesn't really seem willing to talk about it.
+
+Social History:
+Mrs. X is doing well in school. She is an A student and wants to be a doctor. She lives with both of her parents.
+
+Physical Exam:
+Vitals:
+Tcurrent 98.7 BP 115/75 HR 60 RR 20 SpO2 99% on room air.
+
+Head Eyes Ears Nose Throat: There is no conjunctivitis. Her tympanic membranes are clear and freely mobile bilaterally, there is no rhinorrhea, nor erythema nor petechiae in the oropharynx. 
+Cardiovascular: No murmors rubs or gallops. Her heart has a regular rate and rhythm. S1 and S2 were appreciated.
+Pulmonary: Her lungs are clear to auscultation bilaterally. There is no wheezing nor rails or rhonchi. She is not recruiting accessory muscles nor does she have a clinically apparent prolonged expiratory phase.
+Gastrointestinal: Her abdomen is non distended without masses appreciable. Normal bowel sounds are present in all four quadrants. Her abdomen is soft and non-tender without rebound or guarding. There is no hepatosplenomegally appreciable on deep palpation, nor any other mass. 
+Lower Extremity: Her lower extremities are well perfused. There is no edema. Her dorsalis pedis and posterior tibial pulses are intact bilaterally. 
+
+Labs/Ancillary:
+There are no labs at time of current encounter.
+
+Assessment and Plan:
+Mrs X is a well appearing cheerful young woman in no acute distress. Her vital signs are stable. She has an unremarkable physical exam. Her history is significant for long standing GERD, a risk factor for esophageal stricture/ring/web. However, she has been on omeprazole and the dysphagia is increasing. Further, she seems to clearly differentiate the long standing GERD from the dysphagia and is familiar with her symptoms enough to state clearly that one does not precede the other. One would think that she would have noticed increasing GERD in the last year. Her food related allergies that seem to localize around her lips and mouth raise a concern for EoE (eosinophilic esophagitis). In any of the cases, the next step in her management should be consultation with a specialist. This would likely lead to either a pH probe, a trial of increased PPIs, or more to the point perhaps, an upper endoscopy with biopsy.

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_FebrileSez_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_FebrileSez_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_FebrileSez_1.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_FebrileSez_1.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,102 @@
+Case description for C-Takes documenting:
+Setting: Inpatient.
+Specialty: Pediatrics. 
+Note detail level (1-5): 5.
+Level of abbreviation (Low/Medium/High): Low.
+
+CC/HPI:  
+X was in her regular state of good health when, at 0200 2 Feb, she awoke crying. Her mother thought she felt hot. She performed an axillary temperature at that time. She reported the temperature to be 104F. She then administered a "children's dose" of Tylenol. The patient reached a temperature of around 101 to 102F. Her mother then took her to the ER. This was around 0900. At the time of assessment in the ER her temperature was 104F. The patient was then taken to the staff pediatrician in the clinic. After a full physical exam revealed no other likely source of infection a urine specimen was collected by catheter. Lab results of this specimen showed >100WBCs and moderate leukocyte esterase. X was ordered at that time for Septra 5mL PO BID and Tylenol 4mL PO q4-6. She was then sent home with these prescriptions. However, the patient vomited the medications. Her mother and she returned to the pediatric clinic for refractory fevers and inability to tolerate PO antibiotics. At this time
  X had a ÒseizureÓ as described by her mother: her eyes rolled up in her head and she went ÒrigidÓ and Òkind of vibratedÓ. This was in the waiting room of the pediatric clinic. The pediatrician was called but the episode was over. The patient was then admitted to 5w due to seizure, failure of outpatient medical management, and inability to tolerate PO medication. 
+
+ROS: 
+Her mother reports decreased feeding. She also reports decreased wet diapers, with only a few "barely wet" ones. Further, she denies lethargy, SOB, pulling at ears, rhinorrhea, or cough. She also denies diarrhea and does not feel there is anything else Òout of the ordinaryÓ.
+
+Past Medical History:  
+The patient was delivered via c-section at 39+5. No infectious risk factors were identified at birth. She showed no signs or symptoms of congenital syndromes or diseases; In other words, the perinatal period was uncomplicated. Since her birth there was one instance of lacrimal duct stenosis that has been resolved and a case of roseola two months ago that has also resolved.
+
+Past Surgical History:  
+No reported past surgical history.
+
+Allergies:
+No known drug or food allergies.
+
+Medications:
+Tylenol 4mL, last dose at 1540 - vomited.
+Septra 4mL, last dose at 1540 - vomited.
+
+Vaccinations:
+Reviewed and current as of 2Feb2013.
+
+Diet:  
+She is currently taking formula, mushed rice and cereal.
+
+Social History: 
+X lives at home with her two brothers, four and seven, two cats, and her mom and dad. She is not enrolled in day-care. Mother and father are happily married. Mother works at a middle school. Father is in the Navy.
+
+Family History: 
+No history of persistent UTI or VUR. No family history of seizure. 
+
+PE:
+Weight on admission: 6.8kg
+Vit: T 104, HR 141, RR 28, SPo2 97% on RA.
+Gen: X is a sick appearing infant female in mild distress. She is clinging to her mother and crying.
+Neuro: There is not any ptosis or facial asymmetry. There are not signs of focal neurologic deficit. Her pupils are equal in size and reactive to light.
+HEENT: Mucous membranes are dry. There is not deformity, swelling, nor hematoma; No venous distention or gaping sutures. Her tympanic membranes are clear bilaterally. There is not erythema or exudate in the pharynx, nor cough. The patientÕs nares are patent bilaterally. There is not rhinorrhea. Her red reflexes are intact bilaterally. There is not any periauricular, occipital, cervical, or submandibular lymphadenopathy. 
+CV: No murmurs rubs or gallops. Her heart has a regular rate and rhythm. 
+Pulm: Her chest is clear to auscultation bilaterally. There are not any wheezes, rales, nor rhonchi. 
+GI: Her abdomen shows no distention and there are normal bowel sounds in all four quadrants. On palpation there are no signs of hepatosplenomegaly. 
+GU: There is not any vaginal discharge. She has normal appearing female genitalia without erythema. 
+MSK: She moves all extremities without impairment. 
+Integumentary: There are not any rashes nor lesions.
+
+Labs/Ancillary:
+
+Urinalysis Site/Specimen
+
+WBC URINE >100 (H) 
+RBC URINE 28 (H) 
+Bacteria URINE OCCASIONAL (H) 
+Mucus URINE RARE 
+Color URINE YELLOW 
+Clarity URINE SLIGHTY CLOUDY 
+pH URINE 6.0 
+Specific Gravity URINE 1.016 
+Protein URINE 50 mg/dL (1+) (H) 
+Glucose URINE NEGATIVE 
+Ketones URINE TRACE (H) 
+Bilirubin URINE NEGATIVE 
+Blood URINE SMALL (1+) (H) 
+Nitrite URINE NEGATIVE 
+Urobilinogen URINE NORMAL 
+Leukocyte Esterase URINE MODERATE (H) 
+
+Problem list:
+Inability to feed. 
+Low diaper count. 
+Labs concerning for UTI. 
+Fever.
+Vomiting. 
+Seizure. 
+
+A/P:  
+X is an 8 month old female in mild distress who appears ill. She has had a two day history of high fever and a likely episode of febrile seizure. She also has a UA concerning for UTI and is very volume-down. There is not any lethargy at this time nor focal neurologic deficits/signs nor continued seizure. However, she is unable to tolerate anything PO. Her vital signs are otherwise stable. 
+
+1. UTI w/ fevers and seizures:
+- IV access, CBC, blood cultures x1
+- Rocephin 50mg/kg IV daily. Adjust as needed by culture.
+- Tylenol 120mg PR q6.
+- Motrin 85mg PO q8 as tolerated and PRN.
+
+   * Renal Ultrasound to r/o renal scarring and hydronephrosis. 
+   * EEG to r/o seizure disorder. 
+
+2. Dehydration:
+- IVF:  mIVF D51/4NS @35cc/h.
+- I/O:  daily weights and record In/out/diapers.
+- Diet:  Formula and clears Po ad lib.
+
+3. Seizure:
+- With further seizure, spinal tap and culture CSF. 
+
+4. Further workup:
+
+   * If recurrent UTI, w/u for VUR with VCUG.

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_RoutBirthNote_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_RoutBirthNote_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_RoutBirthNote_1.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_RoutBirthNote_1.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,28 @@
+Case description for C-Takes documenting:
+Setting: Outpatient.
+Specialty: Pediatrics. 
+Note detail level (1-5): 3.
+Level of abbreviation (Low/Medium/High): Medium.
+
+18 hour old infant male (Baby X), AGA 3214g born at 40+1 weeks on 0 Feb 2010 at 1400 with apgars of 8/9, routine NRP was performed. Mother is a 26 yo G3nowP3, A+, GBS+, RI, SVD w/ ROM <18 hours. PCN given x2, no other infectious risk factors. Pt requesting routine circ. Overnight: Newborn is breast feeding well, no other issues. Hearing test pending. Pre and post ds pending. Prob no TCB necessary. IMS pending. Wt DOL #2 pending. ABO RH+ not required.
+
+Vit: T 98.2-99.6 HR 98-136 SPO2 97 RR 26-44
+PE:
+Head circ@birth: 33.5
+Gen: Sleeping on initial exam, easily aroused, no acute distress.
+Neuro: Moro, grasp, and sucking reflexes intact. Normal tone.
+Optho: Red reflex present bilat.
+Head: Fontanelle flat, mildly overriding sutures, no evidence of low set ears, holes, tags.
+ENT: Patent nares, no flaring, no signs of cleft pallet. 
+CV: No m/r/g, rrr. S1, S2 wnl. No cyanosis, cap refill wnl. 
+Pulm: Ctab, no w/r/r. No accessory muscle recruitment. 
+Abd: Soft, nbs, non tender, no hepatosplenomegally.
+MSK: Unremarkable Otolinii/Barlow.
+Gen/Uro: Normal appearing male gen.
+Derm: No signs of jaundice, no rashes/lesions, no etn.
+
+A/P: 
+Newborn infant male in no acute distress. Unremarkable exam. Doing well.
+- Plan circumcision for this AM.
+- Counsel parents on wound care for circumcision.
+- Plan to DC this PM pending normal routine discharge w/u.

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_AAA_Leak_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_AAA_Leak_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_AAA_Leak_1.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_AAA_Leak_1.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,26 @@
+Case description for C-Takes documenting:
+Setting: Outpatient.
+Specialty: Vascular Surgery. 
+Note detail level (1-5): 3.
+Level of abbreviation (Low/Medium/High): Low.
+
+HPI/CC:
+Mr X is a 78 yo white male w/ a PMH significant for diabetes and AAA. PShx significant for an EVAR repair in 2010 of the AAA. He presents to the clinic today for follow up of the EVAR repair by CTA. A mild sack expansion was noted one year ago by CTA as part of follow up to the initial fix. Additionally, Mr X lives alone and recently lost his wife of 32 years. He has complained of some mild buttock pain upon ambulation.
+
+ROS:
+Patient denies any fever, night sweats, n/v. No SOB, chest pain or extremeity pain.
+
+PE:
+Physical exam reveals a well groomed man who appears his stated age.
+CV: No m/r/g.
+Pulm: CTAB.
+Ext/Vasc: No carotid bruits. No LE edema. Brachial/Radial pulses intact. Dp/Pt: Dp palpable bilaterally, Pt by doppler, biphasic bilaterally. Good cap refill bilat.
+
+Lab/Anc:
+CTA: Endoleak (Type Ib?) w/ slight inc in diam of AAA w/ possbile retrograde flow from right common iliac.
+US Duplx:
+1/13: A-P 5.5, Cor 5.77.
+7/12: A-P 5.2, Cor 5.31.
+
+A/P:
+Mr X is a 78 yo white male, doing well generally, but for the slow expansion of the excluded aneurysmal sack by possible type Ib endleak. Schedule for arteriogram for potential placement of extension of the right limb of the existing graft.

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_FollowUp_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_FollowUp_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_FollowUp_1.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_FollowUp_1.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,28 @@
+Case description for C-Takes documenting:
+Setting: Outpatient.
+Specialty: Vascular Surgery. 
+Note detail level (1-5): 2.
+Level of abbreviation (Low/Medium/High): High.
+
+CC/HPI:
+Mr X is a 77 yo white male w/ a PMH sig. for 3 strokes, 20 year history of diabetes, chronic COPD, PShx sig. for a bilat. aortofem bypass in 2005, and TAA repair at UCSF in Feb 2011. CT angio was n/s for expansion, however I am concerned about his LEs.
+
+ROS:
+Unremarkable with the exception of his vasc/LE exam and known SOB associated with COPD. 
+
+PE:
+Mr X is a well appearing 78 yo male A&Ox3.
+Vit: BP L 140/68, R 159/77, AFVSS.
+Card: No r/m/g, rrr.
+Neuro: Hx of three strokes->neuro deficits wo change.
+Pulm: SOB associated with his long standing emphysema. No w/r/r. Ctab.
+Abd: Nbs, non tender, non distended.
+LE/Vasc: Dependent rubor consistent with long standing dbx. No edema. No claudication. BP significantly lower on L than R. R radial pulse barely palpable, Pop a. not palpable bilat, dp/pt not palpable and not appreciated by doppler. Cap refill >5sec. Feet cold to touch. No claudication, however. Sensation intact bilat.
+
+Lab/Anc:
+CTA of repaired TAA NS for expansion.
+
+A/P:
+Mr X is 5 months s/p TAA repair at UCSF. CTA of endograft not significant for expansion.
+- Follow up in 3 months.
+- CTA prior to followup.
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_PVD_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_PVD_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_PVD_1.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_PVD_1.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,38 @@
+Case description for C-Takes documenting:
+Setting: Inpatient.
+Specialty: Vascular Surgery. 
+Note detail level (1-5): 3.
+Level of abbreviation (Low/Medium/High): Medium.
+
+Mr. X is a 57 y/o M with a multiple year history of worsening RLE numbness, tingling, and burning pain. He reports this started several years ago and has progressed over the past year to include his foot. His ability to walk has worsened and he cannot even walk half of a block due to pain. He also reports several years of spontaneous ulcers on his shins and now a new ulcer to his right 2nd toe over the past 3 weeks. Patient denies any trauma or skin opening to that area. Patient was seen by a podiatrist who started him on Augmentin and a topical antifungal over 1 week ago.
+
+ROS:
+Patient denies any other symptoms to include fevers, chills shortness of breath, chest pain, nausea, vomiting, abdominal pain, constipation, diarrhea, melena, rashes, peripheral edema.
+
+PMH: HTN, peripheral neuropathy, alcohol use, Crohn's disease, diverticulosis, OA.
+
+PSH: Multiple pilonidal I&Ds.
+
+Meds: Toprol XL 200mg daily, nifedipine 30mg daily, gabapentin 600mg TID, celebrex 100mg daily, desonide topical 0.05% ointment PRN, vit b12 1g daily, mupirocin 2% to
+wounds BID, vancomycin 125mg QID, azathioprine 150mg daily, humira qweek, ammonium lactate daily, flagyl 250mg QUD.
+
+All: lisinopril.
+
+FH: HTN, DM
+
+SH: Smokes 3 cigars a day x 30 years, drinks multiple shots of alcohol daily, denies illicit drug use. No h/o alcohol withdrawl per patient.
+
+PE:
+Vitals: BP 151/101, HR 75, T 98.3, 98% RA
+Gen: Patient A&Ox4, thin-appearing, appears older than stated age.
+CV: RRR, no r/m/g.
+Resp: CTAB, no wheezing, rhonchi, rales.
+Neuro: RLE with light sensation intact throughout, motor appears intact but pt effort limited due to pain.
+Ext: RLE - Multiple healing and well-healed ulcerations on shin, small, clean superficial ulcer present on dorsum of 2nd right digit over middle phalanx approx 1.5 cm x 0.5 cm. No signs of infection, no purulence.  LLE with similar ulcers to anterior shin, no obvious foot ulcers.
+Vasc: RLE Ð TP palpable (ABI 0.6), DP dopplerable (ABI 0.6). LLE Ð TP and DP palp (ABI >1)
+Labs: WBC 8.3 (15.4 on admission), H/H 11.3/35, lytes unremarkable, Hgb A1C 5.9.
+
+A/P:
+PVD - 57 M with progressively worsening RLE and foot pain and concern for arterial insufficiency.
+-Etiology of foot/shin ulcers and pain is unclear at this time, but vascular disease is high on my index of suspicion. Recommend keeping wound clean and finishing course of antibiotics as already started. We will bring the patient to the vascular surgery clinic in the morning and perform formal ABIs with toe pressures. Pending those results, he may require angiography and intervention tomorrow.
+-We will continue to follow along. Please contact us with questions or concerns.
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-AAA_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-AAA_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-AAA_1.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-AAA_1.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,20 @@
+Case description for C-Takes documenting:
+Setting: Outpatient.
+Specialty: Vascular Surgery. 
+Note detail level (1-5): 1.
+Level of abbreviation (Low/Medium/High): Low.
+
+HPI/CC:
+Mr. X is a 68 yo white male with a PMH significant for MI 6 years ago that was treated with stenting who presents to the clinic today for f/u of aortic duplex scan requested after seeing him to r/o carotid disease on referal from opthamology due to rapidly expanding cataract. Carotid disease was ruled out at last appointment. AAA screening was requested based on age/race/smoking status.
+
+ROS:
+No fevers/chills/night sweats. Pt denies SOB, n/v, Chest pain. No pain on ambulation.
+
+PE:
+No bruits audible at the carotids. Brachial/Radial intact bilaterally. DP's palpable bilat, however PT's were not. On duplex they were found to be loud and audible but biphasic bilat.
+
+Lab/Anc:
+US Duplex was NS for AAA.
+
+A/P:
+Mr X is a 68 year old man who was screened for AAA. He was not found to have a AAA. It is our recommendation that he not need to be seen again for AAA.

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT.rtf (added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT.rtf Sat Oct 15 00:53:39 2016
@@ -0,0 +1,18 @@
+Case description for C-Takes documenting:
+Setting: Outpatient.
+Specialty: Vascular Surgery. 
+Note detail level (1-5): 1.
+Level of abbreviation (Low/Medium/High): High.
+
+HPI/CC: Mrs. X is a 60 yo white female with a PMH significant for HTN, CAD, AFIB, DMtype2 who presents to the clinic today for f/u to r/o a DVT after RLE edema was appreciated on PE at a f/u apt s/p high saphenous vein ligation and stab phlebectomy of the ipsilateral leg around Feb of 2010. Patient expresses concern over sutures remaining at the incision sites as well as a lesion on her L arm that was noted after IV access was attempted by a tech post-op.
+
+ROS: Pt denies cp/sob. Unremarkable otherwise. 
+
+PE: Mrs X is a well appearing woman who appears her stated age. BP-R: 118/76, BP-L: 134/78. Radial pulses 2+ bilaterally. Could not palpate pedal pulses or pop. pulses bilat., however, pedal pulses 2 by doppler.
+
+ANC: Right LE duplex indicates no DVT.
+
+A/P: Mrs X is a 60 yo female presenting to clinic for f/u to r/o a DVT s/p a high ligation of saphenous vein and stab phlebectomy of right leg. Some sutures remained and were removed. Patient was counceled on hot compress therapy for superficial phlebitis and advised that it should resolve with time. Given the exclusion of DVT, no further appointments are necessary.
+
+
+



Mime
View raw message