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From brittfi...@apache.org
Subject svn commit: r1500524 [1/4] - in /ctakes/sandbox/ctakes-scrubber-deid: csv/ data/ data/input/ data/input/cases/ data/input/cases/test/ data/input/cases/train/ data/input/phi/ data/input/phi/test/ data/input/phi/train/ data/input/pubs/ data/input/pubs/pr...
Date Sun, 07 Jul 2013 19:47:53 GMT
Author: brittfitch
Date: Sun Jul  7 19:47:51 2013
New Revision: 1500524

URL: http://svn.apache.org/r1500524
Log:
add csv directory used for bulk loading db.
add data directory with test case, train case, test protege knowtator file, and models for
train and test.

Added:
    ctakes/sandbox/ctakes-scrubber-deid/csv/
    ctakes/sandbox/ctakes-scrubber-deid/data/
    ctakes/sandbox/ctakes-scrubber-deid/data/input/
    ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/
    ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/test/
    ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/test/testcase.xml   (with props)
    ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/train/
    ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/train/traincase.xml   (with props)
    ctakes/sandbox/ctakes-scrubber-deid/data/input/phi/
    ctakes/sandbox/ctakes-scrubber-deid/data/input/phi/test/
    ctakes/sandbox/ctakes-scrubber-deid/data/input/phi/test/testcase.xml.knowtator.xml   (with
props)
    ctakes/sandbox/ctakes-scrubber-deid/data/input/phi/train/
    ctakes/sandbox/ctakes-scrubber-deid/data/input/pubs/
    ctakes/sandbox/ctakes-scrubber-deid/data/input/pubs/processed/
    ctakes/sandbox/ctakes-scrubber-deid/data/input/pubs/txt/
    ctakes/sandbox/ctakes-scrubber-deid/data/input/pubs/xml/
    ctakes/sandbox/ctakes-scrubber-deid/data/models/
    ctakes/sandbox/ctakes-scrubber-deid/data/models/test.arff
    ctakes/sandbox/ctakes-scrubber-deid/data/models/train.arff
    ctakes/sandbox/ctakes-scrubber-deid/data/models/weka_header.txt   (with props)
    ctakes/sandbox/ctakes-scrubber-deid/data/models/weka_header_with_crf.txt   (with props)
    ctakes/sandbox/ctakes-scrubber-deid/data/scrubbed/
    ctakes/sandbox/ctakes-scrubber-deid/data/scrubbed/test/

Added: ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/test/testcase.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/test/testcase.xml?rev=1500524&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/test/testcase.xml (added)
+++ ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/test/testcase.xml Sun Jul  7 19:47:51
2013
@@ -0,0 +1,68 @@
+<Envelope xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"  xsi:noNamespaceSchemaLocation="variable.xsd"
>
+    <Header>
+        <Identifiers>
+            <FirstName>Doe</FirstName>
+            <LastName>John</LastName>
+            <DateOfBirth>1920-01-01</DateOfBirth>
+            <SSN>123456789</SSN>
+            <AccessionNumber>05-0001D</AccessionNumber>
+            <LocalMRN>7654321</LocalMRN>
+            <Source>ANY</Source>
+        </Identifiers>
+    </Header>
+    <Body>
+        <PathologyCase TissueAcquisitionDate="2005-01-01" >
+            <Codes>
+                <Code Source="UMLS">C0011900</Code>
+                <Code Source="UMLS">C0225317</Code>
+            </Codes>
+            <Clinical>
+                <Patient>
+                    <Age Units="years" >92</Age>
+                    <Gender>M</Gender>
+                </Patient>
+            </Clinical>
+            <BillingDiagnosis Type="LightMicroscopy" >
+                <Term Code="T1X010"  Source="SNOMED" ></Term>
+                <Term Code="M88500"  Source="SNOMED" ></Term>
+            </BillingDiagnosis>
+            <Specimen Key="00" Type="Surgical">
+                <SpecimenAcquisitionProcedure>
+                    <Term Code="C0011900" Source="UMLS">DIAGNOSIS</Term>
+                </SpecimenAcquisitionProcedure>
+            <Topology>
+                <Term Code="C0225317" Source="UMLS">Soft tissue</Term>
+            </Topology>
+            <Topology>
+                <Term Code="C0040300" Source="UMLS">tissue</Term>
+            </Topology>
+            <Topology>
+                <Term Code="C0003792" Source="UMLS">arm</Term>
+            </Topology>
+                <Diagnosis>
+                    <Term Code="C0206632" Source="UMLS">Angiolipomas</Term>
+                </Diagnosis>
+            </Specimen>
+            <Specimen Key="1" >
+            </Specimen>
+            <FullReportText><![CDATA[SPECIMEN SUBMITTED: SKIN ARM X 2.Clinical:
 None noted. Gross:
+                The specimen was received fresh labeled with "John Doe" and "arm lesion"
who is a 92 year old patient "1940-01-01" with 123456789 and 7654321 consists of two fragments
of tan soft tissue measuring 1.1 x 1.1 x 1.0 cm and 1.4 x 0.5 x 0.4 cm respectively.
+                The larger lesion is inked in black the smaller lesion is inked in blue,
both fragments of 05-0001D are serially sectioned and entirely submitted as follows: A-B =
larger fragments, C = smaller fragments.
+                Mr. Smith's specimens were reviewed by Mrs. Jane Doe, M.D. on 2009-02-01.
+                Given .7 mg. of something.
+                Patient may be duplicate with social 018100135.  John's possesive test. John
Doe-Smith hyphen test.
+               Test: The NG tube was discontinued on August 16th and the patient was increased
on August 17th.   On August 18th the patient had stable vital signs.
+               Test: Mercy Hospital in Devils Lake, North Dakota. 
+                
+                
+            04/29/09 Dr. Notarealname DIAGNOSIS: Soft tissue, arm  : Lipomas  two . Ms. Fake
Notarealname, M.D.
+            SPECIMEN SUBMITTED: SKIN ARM X 2. DIAGNOSIS: Soft tissue, arm  : Lipomas  two
. Clinical:  None noted. Gross:
+            Patient admitted at 7:30 a.m. Height: 6'01". 11,000.  Given 2% milk p.o.b.i.d.
+            Other specimens collected on 1/20/91, 12/01/05, 10/6/66, 8/9/1985.
+            5+ +K2 +3
+            For more information, call Dr. Peter Venkman at (800) 555-2368.
+            The specimen was received fresh labeled with "John Doe" and "arm lesion" and
consists of two fragments of tan soft tissue measuring 1.1 x 1.1 x 1.0 cm and 1.4 x 0.5 x
0.4 cm respectively. The larger lesion is inked in  black the smaller lesion is inked in blue,
both fragments are serially sectioned and entirely submitted as follows: A-B = larger fragments,
C = smaller fragments. 4/29/09]]>
+            </FullReportText>
+        </PathologyCase>
+    </Body>
+</Envelope>

Propchange: ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/test/testcase.xml
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/train/traincase.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/train/traincase.xml?rev=1500524&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/train/traincase.xml (added)
+++ ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/train/traincase.xml Sun Jul  7 19:47:51
2013
@@ -0,0 +1,68 @@
+<Envelope xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"  xsi:noNamespaceSchemaLocation="variable.xsd"
>
+    <Header>
+        <Identifiers>
+            <FirstName>Doe</FirstName>
+            <LastName>John</LastName>
+            <DateOfBirth>1920-01-01</DateOfBirth>
+            <SSN>123456789</SSN>
+            <AccessionNumber>05-0001D</AccessionNumber>
+            <LocalMRN>7654321</LocalMRN>
+            <Source>ANY</Source>
+        </Identifiers>
+    </Header>
+    <Body>
+        <PathologyCase TissueAcquisitionDate="2005-01-01" >
+            <Codes>
+                <Code Source="UMLS">C0011900</Code>
+                <Code Source="UMLS">C0225317</Code>
+            </Codes>
+            <Clinical>
+                <Patient>
+                    <Age Units="years" >92</Age>
+                    <Gender>M</Gender>
+                </Patient>
+            </Clinical>
+            <BillingDiagnosis Type="LightMicroscopy" >
+                <Term Code="T1X010"  Source="SNOMED" ></Term>
+                <Term Code="M88500"  Source="SNOMED" ></Term>
+            </BillingDiagnosis>
+            <Specimen Key="00" Type="Surgical">
+                <SpecimenAcquisitionProcedure>
+                    <Term Code="C0011900" Source="UMLS">DIAGNOSIS</Term>
+                </SpecimenAcquisitionProcedure>
+            <Topology>
+                <Term Code="C0225317" Source="UMLS">Soft tissue</Term>
+            </Topology>
+            <Topology>
+                <Term Code="C0040300" Source="UMLS">tissue</Term>
+            </Topology>
+            <Topology>
+                <Term Code="C0003792" Source="UMLS">arm</Term>
+            </Topology>
+                <Diagnosis>
+                    <Term Code="C0206632" Source="UMLS">Angiolipomas</Term>
+                </Diagnosis>
+            </Specimen>
+            <Specimen Key="1" >
+            </Specimen>
+            <FullReportText><![CDATA[SPECIMEN SUBMITTED: SKIN ARM X 2.Clinical:
 None noted. Gross:
+                The specimen was received fresh labeled with "John Doe" and "arm lesion"
who is a 92 year old patient "1940-01-01" with 123456789 and 7654321 consists of two fragments
of tan soft tissue measuring 1.1 x 1.1 x 1.0 cm and 1.4 x 0.5 x 0.4 cm respectively.
+                The larger lesion is inked in black the smaller lesion is inked in blue,
both fragments of 05-0001D are serially sectioned and entirely submitted as follows: A-B =
larger fragments, C = smaller fragments.
+                Mr. Smith's specimens were reviewed by Mrs. Jane Doe, M.D. on 2009-02-01.
+                Given .7 mg. of something.
+                Patient may be duplicate with social 018100135.  John's possesive test. John
Doe-Smith hyphen test.
+               Test: The NG tube was discontinued on August 16th and the patient was increased
on August 17th.   On August 18th the patient had stable vital signs.
+               Test: Mercy Hospital in Devils Lake, North Dakota. 
+                
+                
+            04/29/09 Dr. Notarealname DIAGNOSIS: Soft tissue, arm  : Lipomas  two . Ms. Fake
Notarealname, M.D.
+            SPECIMEN SUBMITTED: SKIN ARM X 2. DIAGNOSIS: Soft tissue, arm  : Lipomas  two
. Clinical:  None noted. Gross:
+            Patient admitted at 7:30 a.m. Height: 6'01". 11,000.  Given 2% milk p.o.b.i.d.
+            Other specimens collected on 1/20/91, 12/01/05, 10/6/66, 8/9/1985.
+            5+ +K2 +3
+            For more information, call Dr. Peter Venkman at (800) 555-2368.
+            The specimen was received fresh labeled with "John Doe" and "arm lesion" and
consists of two fragments of tan soft tissue measuring 1.1 x 1.1 x 1.0 cm and 1.4 x 0.5 x
0.4 cm respectively. The larger lesion is inked in  black the smaller lesion is inked in blue,
both fragments are serially sectioned and entirely submitted as follows: A-B = larger fragments,
C = smaller fragments. 4/29/09]]>
+            </FullReportText>
+        </PathologyCase>
+    </Body>
+</Envelope>

Propchange: ctakes/sandbox/ctakes-scrubber-deid/data/input/cases/train/traincase.xml
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-scrubber-deid/data/input/phi/test/testcase.xml.knowtator.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-scrubber-deid/data/input/phi/test/testcase.xml.knowtator.xml?rev=1500524&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-scrubber-deid/data/input/phi/test/testcase.xml.knowtator.xml (added)
+++ ctakes/sandbox/ctakes-scrubber-deid/data/input/phi/test/testcase.xml.knowtator.xml Sun
Jul  7 19:47:51 2013
@@ -0,0 +1,286 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<annotations textSource="testcase.xml">
+  <annotation>
+    <mention id="nci_all_init_Instance_110016" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2021" end="2029" />
+    <spannedText>John Doe</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110018" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2057" end="2059" />
+    <spannedText>92</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110020" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2078" end="2088" />
+    <spannedText>1940-01-01</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110022" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2095" end="2104" />
+    <spannedText>123456789</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110024" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2109" end="2116" />
+    <spannedText>7654321</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110026" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2335" end="2343" />
+    <spannedText>05-0001D</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110028" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2469" end="2474" />
+    <spannedText>Smith</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110030" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2509" end="2517" />
+    <spannedText>Jane Doe</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110032" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2527" end="2537" />
+    <spannedText>2009-02-01</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110034" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2635" end="2644" />
+    <spannedText>018100135</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110036" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2647" end="2651" />
+    <spannedText>John</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110038" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2670" end="2684" />
+    <spannedText>John Doe-Smith</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110040" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2751" end="2762" />
+    <spannedText>August 16th</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110042" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2796" end="2807" />
+    <spannedText>August 17th</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110044" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2814" end="2825" />
+    <spannedText>August 18th</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110046" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2883" end="2897" />
+    <spannedText>Mercy Hospital</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110048" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2901" end="2926" />
+    <spannedText>Devils Lake, North Dakota</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110050" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2975" end="2983" />
+    <spannedText>04/29/09</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110052" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="2988" end="3000" />
+    <spannedText>Notarealname</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110054" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="3051" end="3068" />
+    <spannedText>Fake Notarealname</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110056" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="3329" end="3336" />
+    <spannedText>1/20/91</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110058" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="3338" end="3346" />
+    <spannedText>12/01/05</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110060" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="3348" end="3355" />
+    <spannedText>10/6/66</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110062" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="3357" end="3365" />
+    <spannedText>8/9/1985</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110064" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="3432" end="3445" />
+    <spannedText>Peter Venkman</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110066" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="3449" end="3463" />
+    <spannedText>(800) 555-2368</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110068" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="3523" end="3531" />
+    <spannedText>John Doe</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110070" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="3859" end="3866" />
+    <spannedText>4/29/09</spannedText>
+  </annotation>
+  <annotation>
+    <mention id="nci_all_init_Instance_110072" />
+    <annotator id="nci_all_init_Instance_4">britt fitch, hms</annotator>
+    <span start="531" end="541" />
+    <spannedText>2005-01-01</spannedText>
+  </annotation>
+  <classMention id="nci_all_init_Instance_110072">
+    <mentionClass id="date">date</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110006">
+    <mentionClass id="id">id</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110004">
+    <mentionClass id="date">date</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110002">
+    <mentionClass id="patient">patient</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110000">
+    <mentionClass id="patient">patient</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110056">
+    <mentionClass id="date">date</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110022">
+    <mentionClass id="id">id</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110058">
+    <mentionClass id="date">date</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110020">
+    <mentionClass id="date">date</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110060">
+    <mentionClass id="date">date</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110018">
+    <mentionClass id="age">age</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110062">
+    <mentionClass id="date">date</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110016">
+    <mentionClass id="patient">patient</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110064">
+    <mentionClass id="doctor">doctor</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110014">
+    <mentionClass id="age">age</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110066">
+    <mentionClass id="phone">phone</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110068">
+    <mentionClass id="patient">patient</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110010">
+    <mentionClass id="id">id</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110070">
+    <mentionClass id="date">date</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110008">
+    <mentionClass id="id">id</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110042">
+    <mentionClass id="date">date</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110040">
+    <mentionClass id="date">date</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110046">
+    <mentionClass id="hospital">hospital</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110044">
+    <mentionClass id="date">date</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110050">
+    <mentionClass id="date">date</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110048">
+    <mentionClass id="location">location</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110054">
+    <mentionClass id="doctor">doctor</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110052">
+    <mentionClass id="doctor">doctor</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110026">
+    <mentionClass id="id">id</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110024">
+    <mentionClass id="id">id</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110030">
+    <mentionClass id="doctor">doctor</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110028">
+    <mentionClass id="patient">patient</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110034">
+    <mentionClass id="id">id</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110032">
+    <mentionClass id="date">date</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110038">
+    <mentionClass id="patient">patient</mentionClass>
+  </classMention>
+  <classMention id="nci_all_init_Instance_110036">
+    <mentionClass id="patient">patient</mentionClass>
+  </classMention>
+</annotations>
+

Propchange: ctakes/sandbox/ctakes-scrubber-deid/data/input/phi/test/testcase.xml.knowtator.xml
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