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Posted to commits@ctakes.apache.org by ch...@apache.org on 2013/04/02 19:44:41 UTC
svn commit: r1463641 [7/42] - in /ctakes/trunk: ctakes-assertion-res/
ctakes-assertion-res/.settings/ ctakes-assertion-res/src/
ctakes-assertion-res/src/main/ ctakes-assertion-res/src/main/resources/
ctakes-assertion-res/src/main/resources/org/ ctakes-...
Added: ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak (added)
+++ ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak Tue Apr 2 17:41:30 2013
@@ -0,0 +1,646 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<root>
+<fragments>
+<!-- Modifier Components of Section Headings -->
+ <fragment>
+ <name>admit</name>
+ <expansion>(?:admit(?:ting)?|admission)</expansion>
+ </fragment>
+<fragment>
+ <name>be</name>
+ <expansion>(\s+(?:am|is|are|was|were))</expansion>
+</fragment>
+ <fragment>
+ <name>left-time-mods</name>
+ <expansion>((?:(?:pre-)?<fragment-ref name="admit"/>|current|discharge|follow[\s+\-]?up|home|interim|initial|postpartum|(?:pre|post)op(?:erative)?|transfer)\s+)</expansion>
+ </fragment>
+ <fragment>
+ <name>left-descr-mods</name>
+ <expansion>((?:brief(?:\s+resume\s+of)?|overall|other|additional|pertinent|relevant|(?:list\s+of\s+)?other|plan\s+for|standardized|summary\s+of|doctor(?:\s+\')?s)\s+)</expansion>
+ </fragment>
+<fragment>
+ <name>include</name>
+ <expansion>(\s+(?:include[ds]?))</expansion>
+</fragment>
+ <fragment>
+ <name>right-time-mods</name>
+ <expansion>(\s+(?:(?:(?:UP)?ON|AS|AT|\@|OF|FOR|(?:PRIOR\s+TO)|(?:DURING))\s+(?:(?:(?:THE|THAT|THIS)\s+)?(?:TIME|DAY)\s+OF\s+)?(?:ADMISSION|ADMIT|DEATH|DISCHARGE|TRANSFER|COMPLICATIONS?|HOME|HOSPITALIZATION|OUTPATIENT)))</expansion>
+ </fragment>
+ <fragment>
+ <name>right-descr-mods</name>
+ <expansion>(\s+(?:(?:by\s+(?:problems?|(?:organ\s+)?systems?|issues?|report))|(?:\s+of\s+note)))</expansion>
+ </fragment>
+ <fragment>
+ <name>right-location-mods</name>
+ <expansion>(\s+in\s+the\s+emergency\s+department)</expansion>
+ </fragment>
+<!-- Core Components of Section Headings -->
+<!--HISTORY/SUBJECTIVE-->
+ <fragment>
+ <name>allergies1</name>
+ <expansion>(?:allergies|allergy|adverse\s+drug\s+reactions?)</expansion>
+ </fragment>
+ <fragment>
+ <name>allergies2</name>
+ <expansion>(allergy(\s*\/\s*reaction)?\s+profile)</expansion>
+ </fragment>
+ <fragment>
+ <name>famhistory</name>
+ <expansion>(?:family\s+(?:(?:medical|social)\s+)?history|fhx?|fam\s+hx)</expansion>
+ </fragment>
+ <fragment>
+ <name>sochistory</name>
+ <expansion>(social\s+history|social\s+hx|\bshx?|soc\s*hx|habits)</expansion>
+ </fragment>
+<!--MEDICATIONS-->
+ <fragment>
+ <name>medication1</name>
+ <expansion>(medications?|medication\s*\(\s*s\s*\)|regimen|treatment\s+cycle)</expansion>
+ </fragment>
+ <fragment>
+ <name>medication2</name>
+ <expansion>(meds?)</expansion>
+ </fragment>
+<!--EXAM/LAB/OBJECTIVE-->
+ <fragment>
+ <name>physicalexam1</name>
+ <expansion>((physical|surgical)(\s+exam(ination)?|\s+findings)?|\bpe|\*pe|on\s+exam(ination)?|examination\s+data)</expansion>
+ </fragment>
+ <fragment>
+ <name>physicalexam2</name>
+ <expansion>((daily|patient)\s+status)</expansion>
+ </fragment>
+<!--ASSESSMENT/DISPOSITION/PLAN/INSTRUCTIONS-->
+<!--IN-PATIENT COURSE-->
+<!--DIAGNOSIS-->
+<!--PROCEDURE/TREATMENT-->
+<!--MAYO CLINIC STYLE DATE -->
+ <fragment>
+ <name>time</name>
+ <expansion>(\d?\d\:\d\d[aApP][mM])</expansion>
+ </fragment>
+ <fragment>
+ <name>mayodate</name>
+ <expansion>(([0123])?\d(Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec)(\d\d)?\d\d\s+<fragment-ref name="time"/>)</expansion>
+ </fragment>
+ <fragment>
+ <name>mayodate2</name>
+ <expansion>([01]?\d/\d?\d/(\d\d)?\d\d\s+<fragment-ref name="time"/>)</expansion>
+ </fragment>
+</fragments>
+
+<!-- Section Heading Patterns -->
+<sections>
+ <!-- ADDENDUM -->
+ <section>
+ <regex>((addendum)\s*\:)</regex>
+ <label>addendum</label>
+ </section>
+ <!-- ADMISSION DATE -->
+ <section>
+ <regex>(?:(?:(?:admission\s+date)|(date\s+of\s+admission))\s*\:)</regex>
+ <label>admission date</label>
+ </section>
+ <!-- AGE -->
+ <section>
+ <regex>age\s*\:</regex>
+ <label>age</label>
+ </section>
+ <!-- ALLERGY -->
+ <section>
+ <regex>(?:(?:<fragment-ref name="allergies1"/>|<fragment-ref name="allergies2"/>)\s*\:)</regex>
+ <label>allergy</label>
+ </section>
+ <!-- APPOINTMENTS -->
+ <section>
+ <regex>(((<fragment-ref name="left-time-mods"/>)|(<fragment-ref name="left-descr-mods"/>))?(appointments?(?:\(?:\s+s\s+\))?)\s*(?:\(\s+s\s+\))?\s*\:)</regex>
+ <label>appointments</label>
+ </section>
+ <!-- ASSESSMENT -->
+ <section>
+ <regex>((<fragment-ref name="left-time-mods"/>|<fragment-ref name="left-descr-mods"/>)?(assessment)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>assessment</label>
+ </section>
+ <!-- ASSESSMENT/PLAN -->
+ <section>
+ <regex>(((<fragment-ref name="left-time-mods"/>)|<fragment-ref name="right-descr-mods"/>)?((?:assessment\s*(?:and|\&|\/)\s*plan)|(?:a\s*(?:\&|\/)\s*p))(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>assessment/plan</label>
+ </section>
+ <!-- ATTENDING MD -->
+ <section>
+ <regex>(?:attend(?:ing)?(?:\s+physician)?\s*\:)</regex>
+ <label>attending md</label>
+ </section>
+ <section>
+ <regex ignore-case="false">([A-Z]{2,2}\d{3,3}\/\d{4,4}\s+[A-Z]+\s+([A-Z]\.\s+)?[A-Z]+\s+\,(?:\s+(?:jr|iii)\s*\,\s*)?\s+M\.D\.)\s*\:</regex>
+ <label>attending md</label>
+ </section>
+ <!-- CHIEF COMPLAINT -->
+ <section>
+ <regex find-all="false">(?:(?:chief\s+complaint)|(?:patient\s+states\s+complaint)\s*\:)</regex>
+ <label>chief complaint</label>
+ </section>
+ <!-- CLINICAL FINDINGS -->
+ <section>
+ <regex>((clinical\s+findings?)\s*\:)</regex>
+ <label>clinical findings</label>
+ </section>
+ <!-- CODE STATUS -->
+ <section>
+ <regex find-all="false">(?:((code(?:\s+status)?)\s*\:))</regex>
+ <label>code status</label>
+ </section>
+ <!-- COMMENTS -->
+ <section>
+ <regex>(((?:additional\s+)comments)\s*\:)</regex>
+ <label>comments</label>
+ </section>
+ <!-- COMPLICATIONS -->
+ <section>
+ <regex find-all="false">(?:((complications?)\s*\:))</regex>
+ <label>complications</label>
+ </section>
+ <!--CONDITION -->
+ <section>
+ <regex>((<fragment-ref name="left-time-mods"/>)?(condition)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>condition</label>
+ </section>
+ <!-- CONSULTANTS -->
+ <section>
+ <regex>((consultants?)\s*\:)</regex>
+ <label>consultants</label>
+ </section>
+ <!-- CONSULTATION SUMMARY -->
+ <section>
+ <regex>((consults)\s*\:)</regex>
+ <label>consultation summary</label>
+ </section>
+ <!--DATE OF BIRTH -->
+ <section>
+ <regex>date\s+of\s+birth\s*\:</regex>
+ <label>date of birth</label>
+ </section>
+ <!--DATE OF EXPIRATION -->
+ <section>
+ <regex>date\s+of\s+expiration\s*\:</regex>
+ <label>date of expiration</label>
+ </section>
+ <!-- DIAGNOSES -->
+ <section>
+ <regex>(((?:principal\s+discharge\s+diagnosis\s*;\s*responsible\s+after\s+study\s+for\s+causing\s+admission\s*\)\s?))\s?)</regex>
+ <label>diagnoses</label>
+ </section>
+ <section>
+ <regex>((?:other\s+diagnosis\s*;\s*conditions\s*\,\s*infections\s*,\s*complications\s*,\s*affecting\s+treatment\s*\/?\s*stay)\s?)</regex>
+ <label>diagnoses</label>
+ </section>
+ <section>
+ <regex>(((?:cause\s+of\s+death\s+and\s+)?((?:final|principal|principle|primary|associated|secondary|additional|other)\s+)?(((?:pre-)?admission|admit(?:ting)?|discharge|(?:pre|post)?operative)\s+)?(?:problems\s+and\s+)?diagnos[ei]s(?:\s*\(\s*es\s*\))?)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>diagnoses</label>
+ </section>
+ <!-- DICTATION\/AUTHOR DETAILS -->
+ <section>
+ <regex>((?:(?:(?:entered|dictated)\s+by\b)|dictator)\s*\:)</regex>
+ <label>dictation/author details</label>
+ </section>
+ <section>
+ <regex ignore-case="false">((?:(?:[A-Z]+\.?)\s+)*[A-Z]+\s*\,\s+M\.D\.\s+DICTATING\s+FOR\s*\:)</regex>
+ <label>dictation/author details</label>
+ </section>
+ <section>
+ <regex ignore-case="false">(This\s+report\s+was\s+created\s+by\s+[A-Z])</regex>
+ <label>dictation/author details</label>
+ </section>
+ <!-- DIET -->
+ <section>
+ <regex>((<fragment-ref name="left-time-mods"/>)?(diet)\s*\:)</regex>
+ <label>diet</label>
+ </section>
+ <!-- DISCHARGE ACTIVITY -->
+ <section>
+ <regex>(((?:discharge\s+)?activity)\s*\:)</regex>
+ <label>discharge activity</label>
+ </section>
+ <section>
+ <regex>(^((?:discharge\s+)?activity)\s*)(\n)</regex>
+ <label>discharge activity</label>
+ </section>
+ <!-- DISCHARGE DATE -->
+ <section>
+ <regex>((discharge\s+date)|(date\s+of\s+discharge))\s*\:</regex>
+ <label>discharge date</label>
+ </section>
+ <!-- DISCHARGE DETAILS -->
+ <section>
+ <regex>((discharge\s+patient\s+on)\s*\:)</regex>
+ <label>discharge details</label>
+ </section>
+ <!-- DISCHARGE ORDERS -->
+ <section>
+ <regex>(((?:doctor\'?s\s+)?discharge\s+orders)\s*\:)</regex>
+ <label>discharge orders</label>
+ </section>
+ <!-- DISCHARGE NOTIFICATION SUMMARY -->
+ <section>
+ <regex>(ed\s+discharge\s+notification\s*\/\s*summary)(\s+)</regex>
+ <label>discharge notification summary</label>
+ </section>
+ <!-- DISPOSITION -->
+ <section>
+ <regex>((<fragment-ref name="left-time-mods"/>)?(disposition)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>disposition</label>
+ </section>
+ <!-- EMERGENCY DEPARTMENT COURSE -->
+ <section>
+ <regex>((<fragment-ref name="left-descr-mods"/>)?((?:ed\s+course)|(?:emergency\s+department\s+course)|(?:in\s+(?:the\s+)?ed|\bed))<fragment-ref name="right-descr-mods"/>?(\s*\:|\*+))</regex>
+ <label>emergency department course</label>
+ </section>
+ <!-- EVALUATION DATE -->
+ <section>
+ <regex>evaluation\s+date\s*\:</regex>
+ <label>evaluation date</label>
+ </section>
+ <!-- EVENTS -->
+ <section>
+ <regex>((events)\s*\:)</regex>
+ <label>events</label>
+ </section>
+ <!-- FAMILY HISTORY -->
+ <section>
+ <regex find-all="false">(?:(?:<fragment-ref name="famhistory"/>)\s*\:)</regex>
+ <label>family history</label>
+ </section>
+ <section>
+ <regex ignore-case="false" find-all="false">(?:(?:FAMILY\s+HISTORY\s+[a-z]+))</regex>
+ <label>family history</label>
+ </section>
+ <!-- FOLLOW-UP -->
+ <section>
+ <regex>((discharged?\s+wound\s+care)\s*\:)</regex>
+ <label>discharge wound care</label>
+ </section>
+ <section>
+ <regex>(((?:discharged?\s+follow[\s\-]?up(?:\s+care)?)|((?:standardized\s+)?discharge\s+orders\s+\(\s+medications\s+instructions\s+to\s+patient\s+\,\s+follow-up\s+care\s+\))|(disposition\s*\,\s+follow[\s+\-]up\s+and\s+instructions\s+to\s+patient)|(?:follow[\s\-]?up))\s*\:)</regex>
+ <label>follow-up</label>
+ </section>
+ <section>
+ <regex>((((?:discharged?\s+follow[\s\-]?up(?:\s+care)?))|((?:standardized\s+)?discharge\s+orders\s+\(\s+medications\s+instructions\s+to\s+patient\s+\,\s+follow-up\s+care\s+\))|(disposition\s*\,\s+follow[\s+\-]up\s+and\s+instructions\s+to\s+patient)|(?:follow[\s\-]?up))\s*)(\n)</regex>
+ <label>follow-up</label>
+ </section>
+ <!-- GENDER -->
+ <section>
+ <regex>sex\s*\:</regex>
+ <label>gender</label>
+ </section>
+ <!-- HEALTH STATUS -->
+ <section>
+ <regex>^(health\s+status)\s*(\n)</regex>
+ <label>health status</label>
+ </section>
+ <!-- HISTORY OF PRESENT ILLNESS/REASON FOR HOSPITALIZATION -->
+ <section>
+ <regex>((<fragment-ref name="left-descr-mods"/>)?(?:history\s+(?:of\s+(?:the\s+)?)?(?:present|physical)\s+illness|hpi)\s+and\s+(?:(?:history\s+and\s+)?reasons?\s+(?:for\s+)?(?:hospitalization|admission|admit))\s*\:)</regex>
+ <label>history of present illness/reason for hospitalization</label>
+ </section>
+ <section>
+ <regex>(?:(?:reason|indications)\s+for\s+(?:operation|procedure|hospitalization)\s*\:)</regex>
+ <label>history of present illness/reason for hospitalization</label>
+ </section>
+ <section>
+ <regex find-all="false">((?:(?:history\s+and\s+)?reasons?\s+(?:for\s+)?(?:hospitalization|admission|admit))\s*\:)</regex>
+ <label>reason for hospitalization</label>
+ </section>
+ <section>
+ <regex>((<fragment-ref name="left-descr-mods"/>)?(((history\s+(of\s+(the\s+)?)?)?(present|physical)\s+illness)|hpi)\s*\:)</regex>
+ <label>history of present illness</label>
+ </section>
+ <section>
+ <regex>(((?:history\s+(?:of\s+(?:the\s+)?)?(?:present|physical)\s+illness)|hpi)\s*)\n</regex>
+ <label>history of present illness</label>
+ </section>
+ <section>
+ <regex>(^(<fragment-ref name="left-descr-mods"/>)?((?:clinical\s+)?history)\s*\:)</regex>
+ <label>history of present illness</label>
+ </section>
+ <!-- HOSPITAL COURSE -->
+ <section>
+ <regex>((<fragment-ref name="left-descr-mods"/>)?(?:hosp(?:ital)?\s+course(?:\s+and\s+treatment)?)|(?:summary\s+of\s+hospitalization)<fragment-ref name="right-descr-mods"/>?(\s*\:|\*+|\-+))</regex>
+ <label>hospital course</label>
+ </section>
+ <section>
+ <regex>((<fragment-ref name="left-descr-mods"/>)?(?:hosp(?:ital)?\s+course(?:\s+and\s+treatment)?)|(?:summary\s+of\s+hospitalization)<fragment-ref name="right-descr-mods"/>?)(\s*\n)</regex>
+ <label>hospital course</label>
+ </section>
+ <section>
+ <regex>(\*+(hosp(?:ital)?\s+course(?:\s+and\s+treatment)?)|(?:summary\s+of\s+hospitalization))</regex>
+ <label>hospital course</label>
+ </section>
+ <section>
+ <regex>((hosp(?:ital)?\s+course(\s+and\s+treatment)?)|(summary\s+of\s+hospitalization)<fragment-ref name="right-descr-mods"/>\s+([a-z]+|\())</regex>
+ <label>hospital course</label>
+ </section>
+ <!-- IMPRESSION -->
+ <section>
+ <regex find-all="false">((impressions?|imp)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>impression</label>
+ </section>
+ <!-- IMPRESSION\/PLAN -->
+ <section>
+ <regex>((?:impression\s+and\s+plan)\s*\:)</regex>
+ <label>impression/plan</label>
+ </section>
+ <!-- IMPRESSION\/PLAN -->
+ <section>
+ <regex>((?:impression\s+and\s+plan)\s*)(\n)</regex>
+ <label>impression/plan</label>
+ </section>
+ <!-- INSTRUCTIONS -->
+ <section>
+ <regex>(((<fragment-ref name="left-time-mods"/>)|(<fragment-ref name="left-descr-mods"/>))+(instructions?)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>instructions</label>
+ </section>
+ <section>
+ <regex>(^(instructions?)(<fragment-ref name="right-time-mods"/>)?\s*)(\n)</regex>
+ <label>instructions</label>
+ </section>
+ <!--LABORATORY/STUDIES -->
+ <section>
+ <regex>((?:(<fragment-ref name="left-time-mods"/>)|(<fragment-ref name="left-descr-mods"/>))?((?:summary\s+of\s+)?(?:(?:diagnostic\s+)?(?:laboratory|labs?|laboratories|diagnostic|radiologic)(?:(?:\s+and\s+)|(?:\/))?\s*(?:radiologic\s+)?(?:studies|data|results|exams?(?:inations?)?|evaluation|values|findings|tests?|x\-rays?)?)|(?:tests\/procedures|(?:studies\/(?:procedures|tests))|(?:proc(?:edures)?\/tests)|tests))(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>laboratory</label>
+ </section>
+ <section>
+ <regex>(((?:new|discrete|(?:today\s+\'s))\s+results(?:\s+only)?)\s*\:)</regex>
+ <label>laboratory</label>
+ </section>
+ <section>
+ <regex>(((?:new|discrete|(?:today\s+\'s))\s+results(?:\s+only)?)\s*)\n</regex>
+ <label>laboratory</label>
+ </section>
+ <section>
+ <regex>((<fragment-ref name="left-time-mods"/>)\s*data(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>laboratory</label>
+ </section>
+ <section>
+ <regex>((?:\-+|\*+|\_+)\s*)(data(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>laboratory</label>
+ </section>
+ <!-- MEDICATION -->
+ <section>
+ <regex>(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="medication1"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="be"/>|<fragment-ref name="include"/>)?\s*\:</regex>
+ <label>medication</label>
+ </section>
+ <section>
+ <regex>^(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="medication1"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="be"/>|<fragment-ref name="include"/>)?\s*\n</regex>
+ <label>medication</label>
+ </section>
+ <section>
+ <regex>(<fragment-ref name="left-time-mods"/>)(<fragment-ref name="medication2"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="be"/>|<fragment-ref name="include"/>?\s*\:)</regex>
+ <label>medication</label>
+ </section>
+ <section>
+ <regex>^(<fragment-ref name="medication2"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="be"/>|<fragment-ref name="include"/>?\s*\:)</regex>
+ <label>medication</label>
+ </section>
+ <section>
+ <regex>((<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="medication1"/>)\s+on\s+transfer\s+from(\s+[A-Z]+)+(<fragment-ref name="be"/>|<fragment-ref name="include"/>)?\s*\:)</regex>
+ <label>medication</label>
+ </section>
+ <section>
+ <regex ignore-case="false" >(MEDICATIONS(<fragment-ref name="right-time-mods"/>)?)(\s+[a-z]+)</regex>
+ <label>medication</label>
+ </section>
+ <!--OB-GYN HISTORY -->
+ <section>
+ <regex>(((?:(?:past\s+)?ob\-gyn\s+history))\s*\:)</regex>
+ <label>ob-gyn history</label>
+ </section>
+ <section>
+ <regex>(((?:past\s+obstetric\s+history))\s*\:)</regex>
+ <label>obstetric history</label>
+ </section>
+ <section>
+ <regex>^(((?:past\s+gyn(?:ocologic(?:al)?)?\s+history))\s*\:)</regex>
+ <label>gynocologic history</label>
+ </section>
+ <!-- OBJECTIVE -->
+ <section>
+ <regex find-all="false">(?:objective\s*\:?\n)</regex>
+ <label>objective</label>
+ </section>
+ <section>
+ <regex find-all="false">(?:^o\s*\:\n)</regex>
+ <label>objective</label>
+ </section>
+ <!--OPERATIONS/PROCEDURES -->
+ <section>
+ <regex>(((?:((?:principal|principle|primary|special)\s+)?(?:operations?\s+(?:and|or)\s+)?procedures?(\s+(?:and|or)\s+operations?)?(?:\s+performed)?)|(operations\s*\/\s*procedures)|(?:operations?))\s*\:)</regex>
+ <label>operations/procedures</label>
+ </section>
+ <section>
+ <regex>((((?:associated|secondary|additional|other)\s+)(?:operations?\s+(?:and|or)\s+)?procedures?(\s+(?:and|or)\s+operations?)?)\s*\:)</regex>
+ <label>operations/procedures</label>
+ </section>
+ <section>
+ <regex>((procedure\s+note)\s*\:)</regex>
+ <label>procedure description</label>
+ </section>
+ <section>
+ <regex>((procedure\s+in\s+detail)\s*\:)</regex>
+ <label>procedure description</label>
+ </section>
+ <section>
+ <regex>((postpartum\s+diagnostic\s+procedures)\s*\:)</regex>
+ <label>postpartum diagnostic procedures</label>
+ </section>
+ <section>
+ <regex>((postpartum\s+therapeutic\s+procedures)\s*\:)</regex>
+ <label>postpartum therapeutic procedures</label>
+ </section>
+ <section>
+ <regex>((other\s+postpartum\s+therapies)\s*\:)</regex>
+ <label>other poastpartum treatment</label>
+ </section>
+ <!-- PAST CARDIAC HISTORY -->
+ <section>
+ <regex>((past\s+cardiac\s+history)\s*\:)</regex>
+ <label>past cardiac history</label>
+ </section>
+ <!-- PAST MEDICAL HISTORY -->
+ <section>
+ <regex>(past\s+(medical\s+)?history|medical\s+history|pmhx?|pmedhx)\s*\:</regex>
+ <label>past medical history</label>
+ </section>
+ <section>
+ <regex>((past\s+(?:medical\s+)?history|medical\s+history|pmhx?|pmedhx)\/(<fragment-ref name="sochistory"/>)\s*\:)</regex>
+ <label>past medical history</label>
+ </section>
+ <!-- PAST SURGICAL HISTORY -->
+ <section>
+ <regex>(past\s+surgical\s+history)\s*\:</regex>
+ <label>past surgical history</label>
+ </section>
+ <!-- PATIENT INFO -->
+ <section>
+ <regex ignore-case="false">(\*+\s+(FINAL\s+)?DISCHARGE\s+ORDERS\s+\*+)</regex>
+ <label>patient info</label>
+ </section>
+ <!-- PHYSICAL EXAMINATION -->
+ <section>
+ <regex>((<fragment-ref name="left-descr-mods"/>)?(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="physicalexam1"/>|<fragment-ref name="physicalexam2"/>)(<fragment-ref name="right-time-mods"/>)?<fragment-ref name="right-location-mods"/>?(?:\s*\:|\-[^a-z]))</regex>
+ <label>physical examination</label>
+ </section>
+ <section>
+ <regex>((<fragment-ref name="left-descr-mods"/>)?(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="physicalexam1"/>|<fragment-ref name="physicalexam2"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="right-location-mods"/>)?)((\s+vss?)(?:\s*\:|\-[^a-z]))</regex>
+ <label>physical examination</label>
+ </section>
+ <section>
+ <regex>((?:\-+|\*+|\_+|(<fragment-ref name="left-descr-mods"/>))\s*(?:exam(?:ination)?(?:\s+data)?(<fragment-ref name="right-time-mods"/>)\s*\:))</regex>
+ <label>physical examination</label>
+ </section>
+ <section>
+ <regex>^((<fragment-ref name="left-time-mods"/>)(?:exam(?:ination)?)(?:\s*\:))</regex>
+ <label>physical examination</label>
+ </section>
+ <section>
+ <regex>^((<fragment-ref name="left-descr-mods"/>)?(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="physicalexam1"/>|<fragment-ref name="physicalexam2"/>))(\n)</regex>
+ <label>physical examination</label>
+ </section>
+ <!-- PLAN -->
+ <section>
+ <regex ignore-case="false">(?:^((<fragment-ref name="left-time-mods"/>)?(\bplans?)(\s*\:[^\d]|\s*\*)))</regex>
+ <label>plan</label>
+ </section>
+ <section>
+ <regex ignore-case="false">(?:^((<fragment-ref name="left-time-mods"/>)?(\bplans?))(\s*\n))</regex>
+ <label>plan</label>
+ </section>
+ <!-- PLAN: DISPOSITION/PLAN -->
+ <section>
+ <regex>(((?:disposition\s*(?:and|\&|\/)\s*plan)|(?:disposition\s*(?:\&|\/)plan))(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>plan</label>
+ </section>
+ <!-- PLAN: TO DO\/PLAN -->
+ <section>
+ <regex>(((?:to\s+do\s*\/\s*plans?))\s*\:)</regex>
+ <label>plan</label>
+ </section>
+ <!-- PRELIMINARY REPORT CONTENT -->
+ <section>
+ <regex>(($pch)\s*\:)(\s+)</regex>
+ <label>preliminary report content</label>
+ </section>
+ <!-- PREOPERATIVE STATUS -->
+ <section>
+ <regex>((preoperative\s+(?:cardiac\s+)?status)\s*\:)</regex>
+ <label>preoperative stastus</label>
+ </section>
+ <!-- PREVIOUS CARDIOVASCULAR INTERVENTIONS -->
+ <section>
+ <regex>((previous\s+cardiovascular\s+interventions?)\s*\:)</regex>
+ <label>previous cardiovascular interventions</label>
+ </section>
+ <!-- PRIMARY CARE PHYSICIAN -->
+ <section>
+ <regex find-all="false">(?:pcp\s+name\s*\:)</regex>
+ <label>primary care physician</label>
+ </section>
+ <!-- PROBLEMS -->
+ <section>
+ <regex>(((?:(?:patient\s+)?problem\s+list)|(?:significant\s+problems)|(?:(?:(?:his|her)\s+)?problems\s+and\s+management\s+are\s+as\s+follows) )<fragment-ref name="right-descr-mods"/>?\s*[\:;\*+])</regex>
+ <label>problems</label>
+ </section>
+ <!-- RADIOLOGY -->
+ <section>
+ <regex find-all="false">(?:(?:radiology(?:\s+(?:studies|data|results))?)\s*\:)</regex>
+ <label>radiology</label>
+ </section>
+ <!-- REASON FOR CONSULTATION -->
+ <section>
+ <regex find-all="false">(?:reason\s+(?:for\s+)?consultation\s*\:)</regex>
+ <label>reason for consultation</label>
+ </section>
+ <!-- REPORT STATUS -->
+ <section>
+ <regex>((report\s+status)\s*\:)</regex>
+ <label>report status</label>
+ </section>
+ <!--REVIEW OF SYSTEMS -->
+ <section>
+ <regex find-all="false">(?:(review\s+(?:of\s+)?systems|ros)\s*\:)</regex>
+ <label>review of systems</label>
+ </section>
+ <section>
+ <regex ignore-case="false" find-all="false">(?:(REVIEW\s+OF\s+SYSTEMS)(\s+[a-z]+))</regex>
+ <label>review of systems</label>
+ </section>
+ <!-- SERVICE SPRECIALTY -->
+ <section>
+ <regex find-all="false">(?:service\s*\:)</regex>
+ <label>service specialty</label>
+ </section>
+ <!-- SOCIAL HISTORY -->
+ <section>
+ <regex>(?:^(<fragment-ref name="sochistory"/>)\s*\:)</regex>
+ <label>social history</label>
+ </section>
+ <section>
+ <regex ignore-case="false" find-all="false">(?:((SOCIAL\s+HISTORY|HABITS))(\s+[a-z]+))</regex>
+ <label>social history</label>
+ </section>
+ <!-- SUBJECTIVE -->
+ <section>
+ <regex find-all="false">(?:subjective\s*\:?\n)</regex>
+ <label>subjective</label>
+ </section>
+ <section>
+ <regex find-all="false">(?:^s\s*\:\n)</regex>
+ <label>subjective</label>
+ </section>
+ <!-- TRANSCRIPTION DETAILS -->
+ <section>
+ <regex>(((?:escription\s+document)|batch)\s*\:)</regex>
+ <label>transcription details</label>
+ </section>
+ <!-- TREATMENT -->
+ <section>
+ <regex>(((?:treatment\s+rendered))\s*\:?)</regex>
+ <label>treatment</label>
+ </section>
+ <section>
+ <regex>((((?:other\s+treatments?\s*\/\s*procedures\s+\(\s+not\s+in\s+o\.r\.\s+\)))|(other\s+treatments?\s+and\s+procedures))\s*\:?)</regex>
+ <label>other treatments/procedures</label>
+ </section>
+ <!-- UNIT NUMBER -->
+ <section>
+ <regex find-all="false">(?:unit\s+number\s*\:)</regex>
+ <label>unit number</label>
+ </section>
+ <!-- WORK RETURN -->
+ <section>
+ <regex>((return\s+to\s+work)\s*\:)</regex>
+ <label>work return</label>
+ </section>
+ <!-- SECTIONS for Mayo style radiology reports -->
+ <section>
+ <regex>(?:<fragment-ref name="mayodate"/>\s+Exam\:)</regex>
+ <label>radiology exam type</label>
+ </section>
+ <!-- I don't like using "original report" here as a pattern meant only for radiology exam report, as it may come up in other places -->
+ <section>
+ <regex>(?:ORIGINAL REPORT)</regex>
+ <label>radiology exam report</label>
+ </section>
+ <section>
+ <regex>(?:<fragment-ref name="mayodate2"/>\s+\*+\s+Final\s+\*+)</regex>
+ </section>
+ <section>
+ <regex>(?:Indications\:)</regex>
+ <label>reason for examination</label>
+ </section>
+ <section>
+ <regex>(?:SURGICAL PROCEDURE)</regex>
+ <label>surgical procedure</label>
+ </section>
+</sections>
+</root>
+
Added: ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak2
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak2?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak2 (added)
+++ ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak2 Tue Apr 2 17:41:30 2013
@@ -0,0 +1,646 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<root>
+<fragments>
+<!-- Modifier Components of Section Headings -->
+ <fragment>
+ <name>admit</name>
+ <expansion>(?:admit(?:ting)?|admission)</expansion>
+ </fragment>
+<fragment>
+ <name>be</name>
+ <expansion>(\s+(?:am|is|are|was|were))</expansion>
+</fragment>
+ <fragment>
+ <name>left-time-mods</name>
+ <expansion>((?:(?:pre-)?<fragment-ref name="admit"/>|current|discharge|follow[\s+\-]?up|home|interim|initial|postpartum|(?:pre|post)op(?:erative)?|transfer)\s+)</expansion>
+ </fragment>
+ <fragment>
+ <name>left-descr-mods</name>
+ <expansion>((?:brief(?:\s+resume\s+of)?|overall|other|additional|pertinent|relevant|(?:list\s+of\s+)?other|plan\s+for|standardized|summary\s+of|doctor(?:\s+\')?s)\s+)</expansion>
+ </fragment>
+<fragment>
+ <name>include</name>
+ <expansion>(\s+(?:include[ds]?))</expansion>
+</fragment>
+ <fragment>
+ <name>right-time-mods</name>
+ <expansion>(\s+(?:(?:(?:UP)?ON|AS|AT|\@|OF|FOR|(?:PRIOR\s+TO)|(?:DURING))\s+(?:(?:(?:THE|THAT|THIS)\s+)?(?:TIME|DAY)\s+OF\s+)?(?:ADMISSION|ADMIT|DEATH|DISCHARGE|TRANSFER|COMPLICATIONS?|HOME|HOSPITALIZATION|OUTPATIENT)))</expansion>
+ </fragment>
+ <fragment>
+ <name>right-descr-mods</name>
+ <expansion>(\s+(?:(?:by\s+(?:problems?|(?:organ\s+)?systems?|issues?|report))|(?:\s+of\s+note)))</expansion>
+ </fragment>
+ <fragment>
+ <name>right-location-mods</name>
+ <expansion>(\s+in\s+the\s+emergency\s+department)</expansion>
+ </fragment>
+<!-- Core Components of Section Headings -->
+<!--HISTORY/SUBJECTIVE-->
+ <fragment>
+ <name>allergies1</name>
+ <expansion>(?:allergies|allergy|adverse\s+drug\s+reactions?)</expansion>
+ </fragment>
+ <fragment>
+ <name>allergies2</name>
+ <expansion>(allergy(\s*\/\s*reaction)?\s+profile)</expansion>
+ </fragment>
+ <fragment>
+ <name>famhistory</name>
+ <expansion>(?:family\s+(?:(?:medical|social)\s+)?history|fhx?|fam\s+hx)</expansion>
+ </fragment>
+ <fragment>
+ <name>sochistory</name>
+ <expansion>(social\s+history|social\s+hx|\bshx?|soc\s*hx|habits)</expansion>
+ </fragment>
+<!--MEDICATIONS-->
+ <fragment>
+ <name>medication1</name>
+ <expansion>(medications?|medication\s*\(\s*s\s*\)|regimen|treatment\s+cycle)</expansion>
+ </fragment>
+ <fragment>
+ <name>medication2</name>
+ <expansion>(meds?)</expansion>
+ </fragment>
+<!--EXAM/LAB/OBJECTIVE-->
+ <fragment>
+ <name>physicalexam1</name>
+ <expansion>((physical|surgical)(\s+exam(ination)?|\s+findings)?|\bpe|\*pe|on\s+exam(ination)?|examination\s+data)</expansion>
+ </fragment>
+ <fragment>
+ <name>physicalexam2</name>
+ <expansion>((daily|patient)\s+status)</expansion>
+ </fragment>
+<!--ASSESSMENT/DISPOSITION/PLAN/INSTRUCTIONS-->
+<!--IN-PATIENT COURSE-->
+<!--DIAGNOSIS-->
+<!--PROCEDURE/TREATMENT-->
+<!--MAYO CLINIC STYLE DATE -->
+ <fragment>
+ <name>time</name>
+ <expansion>(\d?\d\:\d\d[aApP][mM])</expansion>
+ </fragment>
+ <fragment>
+ <name>mayodate</name>
+ <expansion>(([0123])?\d(Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec)(\d\d)?\d\d\s+<fragment-ref name="time"/>)</expansion>
+ </fragment>
+ <fragment>
+ <name>mayodate2</name>
+ <expansion>([01]?\d/\d?\d/(\d\d)?\d\d\s+<fragment-ref name="time"/>)</expansion>
+ </fragment>
+</fragments>
+<!-- Core Components of Section Headings -->
+<!-- Section Heading Patterns -->
+<sections>
+ <!-- ADDENDUM -->
+ <section>
+ <regex>((addendum)\s*\:)</regex>
+ <label>addendum</label>
+ </section>
+ <!-- ADMISSION DATE -->
+ <section>
+ <regex>(?:(?:(?:admission\s+date)|(date\s+of\s+admission))\s*\:)</regex>
+ <label>admission date</label>
+ </section>
+ <!-- AGE -->
+ <section>
+ <regex>age\s*\:</regex>
+ <label>age</label>
+ </section>
+ <!-- ALLERGY -->
+ <section>
+ <regex>(?:(?:<fragment-ref name="allergies1"/>|<fragment-ref name="allergies2"/>)\s*\:)</regex>
+ <label>allergy</label>
+ </section>
+ <!-- APPOINTMENTS -->
+ <section>
+ <regex>(((<fragment-ref name="left-time-mods"/>)|(<fragment-ref name="left-descr-mods"/>))?(appointments?(?:\(?:\s+s\s+\))?)\s*(?:\(\s+s\s+\))?\s*\:)</regex>
+ <label>appointments</label>
+ </section>
+ <!-- ASSESSMENT -->
+ <section>
+ <regex>((<fragment-ref name="left-time-mods"/>|<fragment-ref name="left-descr-mods"/>)?(assessment)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>assessment</label>
+ </section>
+ <!-- ASSESSMENT/PLAN -->
+ <section>
+ <regex>(((<fragment-ref name="left-time-mods"/>)|<fragment-ref name="right-descr-mods"/>)?((?:assessment\s*(?:and|\&|\/)\s*plan)|(?:a\s*(?:\&|\/)\s*p))(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>assessment/plan</label>
+ </section>
+ <!-- ATTENDING MD -->
+ <section>
+ <regex>(?:attend(?:ing)?(?:\s+physician)?\s*\:)</regex>
+ <label>attending md</label>
+ </section>
+ <section>
+ <regex ignore-case="false">([A-Z]{2,2}\d{3,3}\/\d{4,4}\s+[A-Z]+\s+([A-Z]\.\s+)?[A-Z]+\s+\,(?:\s+(?:jr|iii)\s*\,\s*)?\s+M\.D\.)\s*\:</regex>
+ <label>attending md</label>
+ </section>
+ <!-- CHIEF COMPLAINT -->
+ <section>
+ <regex find-all="false">(?:(?:chief\s+complaint)|(?:patient\s+states\s+complaint)\s*\:)</regex>
+ <label>chief complaint</label>
+ </section>
+ <!-- CLINICAL FINDINGS -->
+ <section>
+ <regex>((clinical\s+findings?)\s*\:)</regex>
+ <label>clinical findings</label>
+ </section>
+ <!-- CODE STATUS -->
+ <section>
+ <regex find-all="false">(?:((code(?:\s+status)?)\s*\:))</regex>
+ <label>code status</label>
+ </section>
+ <!-- COMMENTS -->
+ <section>
+ <regex>(((?:additional\s+)comments)\s*\:)</regex>
+ <label>comments</label>
+ </section>
+ <!-- COMPLICATIONS -->
+ <section>
+ <regex find-all="false">(?:((complications?)\s*\:))</regex>
+ <label>complications</label>
+ </section>
+ <!--CONDITION -->
+ <section>
+ <regex>((<fragment-ref name="left-time-mods"/>)?(condition)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>condition</label>
+ </section>
+ <!-- CONSULTANTS -->
+ <section>
+ <regex>((consultants?)\s*\:)</regex>
+ <label>consultants</label>
+ </section>
+ <!-- CONSULTATION SUMMARY -->
+ <section>
+ <regex>((consults)\s*\:)</regex>
+ <label>consultation summary</label>
+ </section>
+ <!--DATE OF BIRTH -->
+ <section>
+ <regex>date\s+of\s+birth\s*\:</regex>
+ <label>date of birth</label>
+ </section>
+ <!--DATE OF EXPIRATION -->
+ <section>
+ <regex>date\s+of\s+expiration\s*\:</regex>
+ <label>date of expiration</label>
+ </section>
+ <!-- DIAGNOSES -->
+ <section>
+ <regex>(((?:principal\s+discharge\s+diagnosis\s*;\s*responsible\s+after\s+study\s+for\s+causing\s+admission\s*\)\s?))\s?)</regex>
+ <label>diagnoses</label>
+ </section>
+ <section>
+ <regex>((?:other\s+diagnosis\s*;\s*conditions\s*\,\s*infections\s*,\s*complications\s*,\s*affecting\s+treatment\s*\/?\s*stay)\s?)</regex>
+ <label>diagnoses</label>
+ </section>
+ <section>
+ <regex>(((?:cause\s+of\s+death\s+and\s+)?((?:final|principal|principle|primary|associated|secondary|additional|other)\s+)?(((?:pre-)?admission|admit(?:ting)?|discharge|(?:pre|post)?operative)\s+)?(?:problems\s+and\s+)?diagnos[ei]s(?:\s*\(\s*es\s*\))?)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>diagnoses</label>
+ </section>
+ <!-- DICTATION\/AUTHOR DETAILS -->
+ <section>
+ <regex>((?:(?:(?:entered|dictated)\s+by\b)|dictator)\s*\:)</regex>
+ <label>dictation/author details</label>
+ </section>
+ <section>
+ <regex ignore-case="false">((?:(?:[A-Z]+\.?)\s+)*[A-Z]+\s*\,\s+M\.D\.\s+DICTATING\s+FOR\s*\:)</regex>
+ <label>dictation/author details</label>
+ </section>
+ <section>
+ <regex ignore-case="false">(This\s+report\s+was\s+created\s+by\s+[A-Z])</regex>
+ <label>dictation/author details</label>
+ </section>
+ <!-- DIET -->
+ <section>
+ <regex>((<fragment-ref name="left-time-mods"/>)?(diet)\s*\:)</regex>
+ <label>diet</label>
+ </section>
+ <!-- DISCHARGE ACTIVITY -->
+ <section>
+ <regex>(((?:discharge\s+)?activity)\s*\:)</regex>
+ <label>discharge activity</label>
+ </section>
+ <section>
+ <regex>(^((?:discharge\s+)?activity)\s*)(\n)</regex>
+ <label>discharge activity</label>
+ </section>
+ <!-- DISCHARGE DATE -->
+ <section>
+ <regex>((discharge\s+date)|(date\s+of\s+discharge))\s*\:</regex>
+ <label>discharge date</label>
+ </section>
+ <!-- DISCHARGE DETAILS -->
+ <section>
+ <regex>((discharge\s+patient\s+on)\s*\:)</regex>
+ <label>discharge details</label>
+ </section>
+ <!-- DISCHARGE ORDERS -->
+ <section>
+ <regex>(((?:doctor\'?s\s+)?discharge\s+orders)\s*\:)</regex>
+ <label>discharge orders</label>
+ </section>
+ <!-- DISCHARGE NOTIFICATION SUMMARY -->
+ <section>
+ <regex>(ed\s+discharge\s+notification\s*\/\s*summary)(\s+)</regex>
+ <label>discharge notification summary</label>
+ </section>
+ <!-- DISPOSITION -->
+ <section>
+ <regex>((<fragment-ref name="left-time-mods"/>)?(disposition)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>disposition</label>
+ </section>
+ <!-- EMERGENCY DEPARTMENT COURSE -->
+ <section>
+ <regex>((<fragment-ref name="left-descr-mods"/>)?((?:ed\s+course)|(?:emergency\s+department\s+course)|(?:in\s+(?:the\s+)?ed|\bed))<fragment-ref name="right-descr-mods"/>?(\s*\:|\*+))</regex>
+ <label>emergency department course</label>
+ </section>
+ <!-- EVALUATION DATE -->
+ <section>
+ <regex>evaluation\s+date\s*\:</regex>
+ <label>evaluation date</label>
+ </section>
+ <!-- EVENTS -->
+ <section>
+ <regex>((events)\s*\:)</regex>
+ <label>events</label>
+ </section>
+ <!-- FAMILY HISTORY -->
+ <section>
+ <regex find-all="false">(?:(?:<fragment-ref name="famhistory"/>)\s*\:)</regex>
+ <label>family history</label>
+ </section>
+ <section>
+ <regex ignore-case="false" find-all="false">(?:(?:FAMILY\s+HISTORY\s+[a-z]+))</regex>
+ <label>family history</label>
+ </section>
+ <!-- FOLLOW-UP -->
+ <section>
+ <regex>((discharged?\s+wound\s+care)\s*\:)</regex>
+ <label>discharge wound care</label>
+ </section>
+ <section>
+ <regex>(((?:discharged?\s+follow[\s\-]?up(?:\s+care)?)|((?:standardized\s+)?discharge\s+orders\s+\(\s+medications\s+instructions\s+to\s+patient\s+\,\s+follow-up\s+care\s+\))|(disposition\s*\,\s+follow[\s+\-]up\s+and\s+instructions\s+to\s+patient)|(?:follow[\s\-]?up))\s*\:)</regex>
+ <label>follow-up</label>
+ </section>
+ <section>
+ <regex>((((?:discharged?\s+follow[\s\-]?up(?:\s+care)?))|((?:standardized\s+)?discharge\s+orders\s+\(\s+medications\s+instructions\s+to\s+patient\s+\,\s+follow-up\s+care\s+\))|(disposition\s*\,\s+follow[\s+\-]up\s+and\s+instructions\s+to\s+patient)|(?:follow[\s\-]?up))\s*)(\n)</regex>
+ <label>follow-up</label>
+ </section>
+ <!-- GENDER -->
+ <section>
+ <regex>sex\s*\:</regex>
+ <label>gender</label>
+ </section>
+ <!-- HEALTH STATUS -->
+ <section>
+ <regex>^(health\s+status)\s*(\n)</regex>
+ <label>health status</label>
+ </section>
+ <!-- HISTORY OF PRESENT ILLNESS/REASON FOR HOSPITALIZATION -->
+ <section>
+ <regex>((<fragment-ref name="left-descr-mods"/>)?(?:history\s+(?:of\s+(?:the\s+)?)?(?:present|physical)\s+illness|hpi)\s+and\s+(?:(?:history\s+and\s+)?reasons?\s+(?:for\s+)?(?:hospitalization|admission|admit))\s*\:)</regex>
+ <label>history of present illness/reason for hospitalization</label>
+ </section>
+ <section>
+ <regex>(?:(?:reason|indications)\s+for\s+(?:operation|procedure|hospitalization)\s*\:)</regex>
+ <label>history of present illness/reason for hospitalization</label>
+ </section>
+ <section>
+ <regex find-all="false">((?:(?:history\s+and\s+)?reasons?\s+(?:for\s+)?(?:hospitalization|admission|admit))\s*\:)</regex>
+ <label>reason for hospitalization</label>
+ </section>
+ <section>
+ <regex>((<fragment-ref name="left-descr-mods"/>)?(((history\s+(of\s+(the\s+)?)?)?(present|physical)\s+illness)|hpi)\s*\:)</regex>
+ <label>history of present illness</label>
+ </section>
+ <section>
+ <regex>(((?:history\s+(?:of\s+(?:the\s+)?)?(?:present|physical)\s+illness)|hpi)\s*)\n</regex>
+ <label>history of present illness</label>
+ </section>
+ <section>
+ <regex>(^(<fragment-ref name="left-descr-mods"/>)?((?:clinical\s+)?history)\s*\:)</regex>
+ <label>history of present illness</label>
+ </section>
+ <!-- HOSPITAL COURSE -->
+ <section>
+ <regex>((<fragment-ref name="left-descr-mods"/>)?(?:hosp(?:ital)?\s+course(?:\s+and\s+treatment)?)|(?:summary\s+of\s+hospitalization)<fragment-ref name="right-descr-mods"/>?(\s*\:|\*+|\-+))</regex>
+ <label>hospital course</label>
+ </section>
+ <section>
+ <regex>((<fragment-ref name="left-descr-mods"/>)?(?:hosp(?:ital)?\s+course(?:\s+and\s+treatment)?)|(?:summary\s+of\s+hospitalization)<fragment-ref name="right-descr-mods"/>?)(\s*\n)</regex>
+ <label>hospital course</label>
+ </section>
+ <section>
+ <regex>(\*+(hosp(?:ital)?\s+course(?:\s+and\s+treatment)?)|(?:summary\s+of\s+hospitalization))</regex>
+ <label>hospital course</label>
+ </section>
+ <section>
+ <regex>((hosp(?:ital)?\s+course(\s+and\s+treatment)?)|(summary\s+of\s+hospitalization)<fragment-ref name="right-descr-mods"/>\s+([a-z]+|\())</regex>
+ <label>hospital course</label>
+ </section>
+ <!-- IMPRESSION -->
+ <section>
+ <regex find-all="false">((impressions?|imp)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>impression</label>
+ </section>
+ <!-- IMPRESSION\/PLAN -->
+ <section>
+ <regex>((?:impression\s+and\s+plan)\s*\:)</regex>
+ <label>impression/plan</label>
+ </section>
+ <!-- IMPRESSION\/PLAN -->
+ <section>
+ <regex>((?:impression\s+and\s+plan)\s*)(\n)</regex>
+ <label>impression/plan</label>
+ </section>
+ <!-- INSTRUCTIONS -->
+ <section>
+ <regex>(((<fragment-ref name="left-time-mods"/>)|(<fragment-ref name="left-descr-mods"/>))+(instructions?)(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>instructions</label>
+ </section>
+ <section>
+ <regex>(^(instructions?)(<fragment-ref name="right-time-mods"/>)?\s*)(\n)</regex>
+ <label>instructions</label>
+ </section>
+ <!--LABORATORY/STUDIES -->
+ <section>
+ <regex>((?:(<fragment-ref name="left-time-mods"/>)|(<fragment-ref name="left-descr-mods"/>))?((?:summary\s+of\s+)?(?:(?:diagnostic\s+)?(?:laboratory|labs?|laboratories|diagnostic|radiologic)(?:(?:\s+and\s+)|(?:\/))?\s*(?:radiologic\s+)?(?:studies|data|results|exams?(?:inations?)?|evaluation|values|findings|tests?|x\-rays?)?)|(?:tests\/procedures|(?:studies\/(?:procedures|tests))|(?:proc(?:edures)?\/tests)|tests))(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>laboratory</label>
+ </section>
+ <section>
+ <regex>(((?:new|discrete|(?:today\s+\'s))\s+results(?:\s+only)?)\s*\:)</regex>
+ <label>laboratory</label>
+ </section>
+ <section>
+ <regex>(((?:new|discrete|(?:today\s+\'s))\s+results(?:\s+only)?)\s*)\n</regex>
+ <label>laboratory</label>
+ </section>
+ <section>
+ <regex>((<fragment-ref name="left-time-mods"/>)\s*data(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>laboratory</label>
+ </section>
+ <section>
+ <regex>((?:\-+|\*+|\_+)\s*)(data(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>laboratory</label>
+ </section>
+ <!-- MEDICATION -->
+ <section>
+ <regex>(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="medication1"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="be"/>|<fragment-ref name="include"/>)?\s*\:</regex>
+ <label>medication</label>
+ </section>
+ <section>
+ <regex>^(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="medication1"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="be"/>|<fragment-ref name="include"/>)?\s*\n</regex>
+ <label>medication</label>
+ </section>
+ <section>
+ <regex>(<fragment-ref name="left-time-mods"/>)(<fragment-ref name="medication2"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="be"/>|<fragment-ref name="include"/>?\s*\:)</regex>
+ <label>medication</label>
+ </section>
+ <section>
+ <regex>^(<fragment-ref name="medication2"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="be"/>|<fragment-ref name="include"/>?\s*\:)</regex>
+ <label>medication</label>
+ </section>
+ <section>
+ <regex>((<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="medication1"/>)\s+on\s+transfer\s+from(\s+[A-Z]+)+(<fragment-ref name="be"/>|<fragment-ref name="include"/>)?\s*\:)</regex>
+ <label>medication</label>
+ </section>
+ <section>
+ <regex ignore-case="false" >(MEDICATIONS(<fragment-ref name="right-time-mods"/>)?)(\s+[a-z]+)</regex>
+ <label>medication</label>
+ </section>
+ <!--OB-GYN HISTORY -->
+ <section>
+ <regex>(((?:(?:past\s+)?ob\-gyn\s+history))\s*\:)</regex>
+ <label>ob-gyn history</label>
+ </section>
+ <section>
+ <regex>(((?:past\s+obstetric\s+history))\s*\:)</regex>
+ <label>obstetric history</label>
+ </section>
+ <section>
+ <regex>^(((?:past\s+gyn(?:ocologic(?:al)?)?\s+history))\s*\:)</regex>
+ <label>gynocologic history</label>
+ </section>
+ <!-- OBJECTIVE -->
+ <section>
+ <regex find-all="false">(?:objective\s*\:?\n)</regex>
+ <label>objective</label>
+ </section>
+ <section>
+ <regex find-all="false">(?:^o\s*\:\n)</regex>
+ <label>objective</label>
+ </section>
+ <!--OPERATIONS/PROCEDURES -->
+ <section>
+ <regex>(((?:((?:principal|principle|primary|special)\s+)?(?:operations?\s+(?:and|or)\s+)?procedures?(\s+(?:and|or)\s+operations?)?(?:\s+performed)?)|(operations\s*\/\s*procedures)|(?:operations?))\s*\:)</regex>
+ <label>operations/procedures</label>
+ </section>
+ <section>
+ <regex>((((?:associated|secondary|additional|other)\s+)(?:operations?\s+(?:and|or)\s+)?procedures?(\s+(?:and|or)\s+operations?)?)\s*\:)</regex>
+ <label>operations/procedures</label>
+ </section>
+ <section>
+ <regex>((procedure\s+note)\s*\:)</regex>
+ <label>procedure description</label>
+ </section>
+ <section>
+ <regex>((procedure\s+in\s+detail)\s*\:)</regex>
+ <label>procedure description</label>
+ </section>
+ <section>
+ <regex>((postpartum\s+diagnostic\s+procedures)\s*\:)</regex>
+ <label>postpartum diagnostic procedures</label>
+ </section>
+ <section>
+ <regex>((postpartum\s+therapeutic\s+procedures)\s*\:)</regex>
+ <label>postpartum therapeutic procedures</label>
+ </section>
+ <section>
+ <regex>((other\s+postpartum\s+therapies)\s*\:)</regex>
+ <label>other poastpartum treatment</label>
+ </section>
+ <!-- PAST CARDIAC HISTORY -->
+ <section>
+ <regex>((past\s+cardiac\s+history)\s*\:)</regex>
+ <label>past cardiac history</label>
+ </section>
+ <!-- PAST MEDICAL HISTORY -->
+ <section>
+ <regex>(past\s+(medical\s+)?history|medical\s+history|pmhx?|pmedhx)\s*\:</regex>
+ <label>past medical history</label>
+ </section>
+ <section>
+ <regex>((past\s+(?:medical\s+)?history|medical\s+history|pmhx?|pmedhx)\/(<fragment-ref name="sochistory"/>)\s*\:)</regex>
+ <label>past medical history</label>
+ </section>
+ <!-- PAST SURGICAL HISTORY -->
+ <section>
+ <regex>(past\s+surgical\s+history)\s*\:</regex>
+ <label>past surgical history</label>
+ </section>
+ <!-- PATIENT INFO -->
+ <section>
+ <regex ignore-case="false">(\*+\s+(FINAL\s+)?DISCHARGE\s+ORDERS\s+\*+)</regex>
+ <label>patient info</label>
+ </section>
+ <!-- PHYSICAL EXAMINATION -->
+ <section>
+ <regex>((<fragment-ref name="left-descr-mods"/>)?(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="physicalexam1"/>|<fragment-ref name="physicalexam2"/>)(<fragment-ref name="right-time-mods"/>)?<fragment-ref name="right-location-mods"/>?(?:\s*\:|\-[^a-z]))</regex>
+ <label>physical examination</label>
+ </section>
+ <section>
+ <regex>((<fragment-ref name="left-descr-mods"/>)?(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="physicalexam1"/>|<fragment-ref name="physicalexam2"/>)(<fragment-ref name="right-time-mods"/>)?(<fragment-ref name="right-location-mods"/>)?)((\s+vss?)(?:\s*\:|\-[^a-z]))</regex>
+ <label>physical examination</label>
+ </section>
+ <section>
+ <regex>((?:\-+|\*+|\_+|(<fragment-ref name="left-descr-mods"/>))\s*(?:exam(?:ination)?(?:\s+data)?(<fragment-ref name="right-time-mods"/>)\s*\:))</regex>
+ <label>physical examination</label>
+ </section>
+ <section>
+ <regex>^((<fragment-ref name="left-time-mods"/>)(?:exam(?:ination)?)(?:\s*\:))</regex>
+ <label>physical examination</label>
+ </section>
+ <section>
+ <regex>^((<fragment-ref name="left-descr-mods"/>)?(<fragment-ref name="left-time-mods"/>)?(<fragment-ref name="physicalexam1"/>|<fragment-ref name="physicalexam2"/>))(\n)</regex>
+ <label>physical examination</label>
+ </section>
+ <!-- PLAN -->
+ <section>
+ <regex ignore-case="false">(?:^((<fragment-ref name="left-time-mods"/>)?(\bplans?)(\s*\:[^\d]|\s*\*)))</regex>
+ <label>plan</label>
+ </section>
+ <section>
+ <regex ignore-case="false">(?:^((<fragment-ref name="left-time-mods"/>)?(\bplans?))(\s*\n))</regex>
+ <label>plan</label>
+ </section>
+ <!-- PLAN: DISPOSITION/PLAN -->
+ <section>
+ <regex>(((?:disposition\s*(?:and|\&|\/)\s*plan)|(?:disposition\s*(?:\&|\/)plan))(<fragment-ref name="right-time-mods"/>)?\s*\:)</regex>
+ <label>plan</label>
+ </section>
+ <!-- PLAN: TO DO\/PLAN -->
+ <section>
+ <regex>(((?:to\s+do\s*\/\s*plans?))\s*\:)</regex>
+ <label>plan</label>
+ </section>
+ <!-- PRELIMINARY REPORT CONTENT -->
+ <section>
+ <regex>(($pch)\s*\:)(\s+)</regex>
+ <label>preliminary report content</label>
+ </section>
+ <!-- PREOPERATIVE STATUS -->
+ <section>
+ <regex>((preoperative\s+(?:cardiac\s+)?status)\s*\:)</regex>
+ <label>preoperative stastus</label>
+ </section>
+ <!-- PREVIOUS CARDIOVASCULAR INTERVENTIONS -->
+ <section>
+ <regex>((previous\s+cardiovascular\s+interventions?)\s*\:)</regex>
+ <label>previous cardiovascular interventions</label>
+ </section>
+ <!-- PRIMARY CARE PHYSICIAN -->
+ <section>
+ <regex find-all="false">(?:pcp\s+name\s*\:)</regex>
+ <label>primary care physician</label>
+ </section>
+ <!-- PROBLEMS -->
+ <section>
+ <regex>(((?:(?:patient\s+)?problem\s+list)|(?:significant\s+problems)|(?:(?:(?:his|her)\s+)?problems\s+and\s+management\s+are\s+as\s+follows) )<fragment-ref name="right-descr-mods"/>?\s*[\:;\*+])</regex>
+ <label>problems</label>
+ </section>
+ <!-- RADIOLOGY -->
+ <section>
+ <regex find-all="false">(?:(?:radiology(?:\s+(?:studies|data|results))?)\s*\:)</regex>
+ <label>radiology</label>
+ </section>
+ <!-- REASON FOR CONSULTATION -->
+ <section>
+ <regex find-all="false">(?:reason\s+(?:for\s+)?consultation\s*\:)</regex>
+ <label>reason for consultation</label>
+ </section>
+ <!-- REPORT STATUS -->
+ <section>
+ <regex>((report\s+status)\s*\:)</regex>
+ <label>report status</label>
+ </section>
+ <!--REVIEW OF SYSTEMS -->
+ <section>
+ <regex find-all="false">(?:(review\s+(?:of\s+)?systems|ros)\s*\:)</regex>
+ <label>review of systems</label>
+ </section>
+ <section>
+ <regex ignore-case="false" find-all="false">(?:(REVIEW\s+OF\s+SYSTEMS)(\s+[a-z]+))</regex>
+ <label>review of systems</label>
+ </section>
+ <!-- SERVICE SPRECIALTY -->
+ <section>
+ <regex find-all="false">(?:service\s*\:)</regex>
+ <label>service specialty</label>
+ </section>
+ <!-- SOCIAL HISTORY -->
+ <section>
+ <regex>(?:^(<fragment-ref name="sochistory"/>)\s*\:)</regex>
+ <label>social history</label>
+ </section>
+ <section>
+ <regex ignore-case="false" find-all="false">(?:((SOCIAL\s+HISTORY|HABITS))(\s+[a-z]+))</regex>
+ <label>social history</label>
+ </section>
+ <!-- SUBJECTIVE -->
+ <section>
+ <regex find-all="false">(?:subjective\s*\:?\n)</regex>
+ <label>subjective</label>
+ </section>
+ <section>
+ <regex find-all="false">(?:^s\s*\:\n)</regex>
+ <label>subjective</label>
+ </section>
+ <!-- TRANSCRIPTION DETAILS -->
+ <section>
+ <regex>(((?:escription\s+document)|batch)\s*\:)</regex>
+ <label>transcription details</label>
+ </section>
+ <!-- TREATMENT -->
+ <section>
+ <regex>(((?:treatment\s+rendered))\s*\:?)</regex>
+ <label>treatment</label>
+ </section>
+ <section>
+ <regex>((((?:other\s+treatments?\s*\/\s*procedures\s+\(\s+not\s+in\s+o\.r\.\s+\)))|(other\s+treatments?\s+and\s+procedures))\s*\:?)</regex>
+ <label>other treatments/procedures</label>
+ </section>
+ <!-- UNIT NUMBER -->
+ <section>
+ <regex find-all="false">(?:unit\s+number\s*\:)</regex>
+ <label>unit number</label>
+ </section>
+ <!-- WORK RETURN -->
+ <section>
+ <regex>((return\s+to\s+work)\s*\:)</regex>
+ <label>work return</label>
+ </section>
+ <!-- SECTIONS for Mayo style radiology reports -->
+ <section>
+ <regex>(?:<fragment-ref name="mayodate"/>\s+Exam\:)</regex>
+ <label>radiology exam type</label>
+ </section>
+ <!-- I don't like using "original report" here as a pattern meant only for radiology exam report, as it may come up in other places -->
+ <section>
+ <regex>(?:ORIGINAL REPORT)</regex>
+ <label>radiology exam report</label>
+ </section>
+ <section>
+ <regex>(?:<fragment-ref name="mayodate2"/>\s+\*+\s+Final\s+\*+)</regex>
+ </section>
+ <section>
+ <regex>(?:Indications\:)</regex>
+ <label>reason for examination</label>
+ </section>
+ <section>
+ <regex>(?:SURGICAL PROCEDURE)</regex>
+ <label>surgical procedure</label>
+ </section>
+</sections>
+</root>
+
Added: ctakes/trunk/ctakes-chunker-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker-res/.classpath?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-chunker-res/.classpath (added)
+++ ctakes/trunk/ctakes-chunker-res/.classpath Tue Apr 2 17:41:30 2013
@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/classes" path="src/main/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/test-classes" path="src/test/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
Added: ctakes/trunk/ctakes-chunker-res/.project
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker-res/.project?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-chunker-res/.project (added)
+++ ctakes/trunk/ctakes-chunker-res/.project Tue Apr 2 17:41:30 2013
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>ctakes-chunker-res</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.m2e.core.maven2Builder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ <nature>org.eclipse.m2e.core.maven2Nature</nature>
+ </natures>
+</projectDescription>
Added: ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.core.resources.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.core.resources.prefs (added)
+++ ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.core.resources.prefs Tue Apr 2 17:41:30 2013
@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
+encoding//src/test/java=UTF-8
+encoding/<project>=UTF-8
Added: ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.jdt.core.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.jdt.core.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.jdt.core.prefs (added)
+++ ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.jdt.core.prefs Tue Apr 2 17:41:30 2013
@@ -0,0 +1,88 @@
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+org.eclipse.jdt.core.compiler.problem.unusedWarningToken=ignore
+org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
+org.eclipse.jdt.core.compiler.source=1.6
Added: ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.ltk.core.refactoring.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.ltk.core.refactoring.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.ltk.core.refactoring.prefs (added)
+++ ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.ltk.core.refactoring.prefs Tue Apr 2 17:41:30 2013
@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+org.eclipse.ltk.core.refactoring.enable.project.refactoring.history=false
Added: ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.m2e.core.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.m2e.core.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.m2e.core.prefs (added)
+++ ctakes/trunk/ctakes-chunker-res/.settings/org.eclipse.m2e.core.prefs Tue Apr 2 17:41:30 2013
@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1
Added: ctakes/trunk/ctakes-chunker-res/LICENSE
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker-res/LICENSE?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-chunker-res/LICENSE (added)
+++ ctakes/trunk/ctakes-chunker-res/LICENSE Tue Apr 2 17:41:30 2013
@@ -0,0 +1,202 @@
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+ names, trademarks, service marks, or product names of the Licensor,
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+ 7. Disclaimer of Warranty. Unless required by applicable law or
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+ Contributor provides its Contributions) on an "AS IS" BASIS,
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+ 8. Limitation of Liability. In no event and under no legal theory,
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+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
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Added: ctakes/trunk/ctakes-chunker-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker-res/pom.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-chunker-res/pom.xml (added)
+++ ctakes/trunk/ctakes-chunker-res/pom.xml Tue Apr 2 17:41:30 2013
@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes</artifactId>
+ <version>3.1.0-SNAPSHOT</version>
+ </parent>
+ <artifactId>ctakes-chunker-res</artifactId>
+ <name>Apache cTAKES Resources ctakes-chunker-res</name>
+ <description>Resources Project for chunker</description>
+</project>
\ No newline at end of file
Added: ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/README
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/README?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/README (added)
+++ ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/README Tue Apr 2 17:41:30 2013
@@ -0,0 +1,24 @@
+
+A chunker model is included with this project.
+
+The model derives from a combination of GENIA, Penn Treebank (Wall Street Journal) and anonymized
+clinical data per Safe Harbor HIPAA guidelines. Prior to model building, the clinical data was
+deidentified for patient names to preserve patient confidentiality. Any person name in the model
+will originate from non-patient data sources.
+
+To build a model of your own, you need to
+1) obtain training data - see data/chunk/genia/README and data/chunk/ptb/README
+2) build a model using the training data.
+
+After you have obtained training data, you can build a chunker model by running the following:
+
+java opennlp.tools.chunker.ChunkerME <training-data> <model-name> <iterations> <cutoff>
+where <training-data> is an OpenNLP training data file as described in e.g. data/chunk/genia/README
+ <model-name> The file name of the resulting model. The name should end with either '.txt'
+ (for a plain text model) or '.bin.gz' (for a compressed binary model).
+ <iterations> How many training iterations will be performed. The default is 100.
+ <cutoff> The minimum number of times a feature has to be seen to be considered for
+ inclusion in the model. The default cutoff is 5.
+
+The arguments <iterations> and <cutoff> are, taken together, optional - i.e. you should provide
+both or provide neither.
Added: ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/chunk-model.claims-1.5.zip
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/chunk-model.claims-1.5.zip?rev=1463641&view=auto
==============================================================================
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------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added: ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/small/chunker.model.bin.gz
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/small/chunker.model.bin.gz?rev=1463641&view=auto
==============================================================================
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------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added: ctakes/trunk/ctakes-constituency-parser-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/.classpath?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/.classpath (added)
+++ ctakes/trunk/ctakes-constituency-parser-res/.classpath Tue Apr 2 17:41:30 2013
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/classes" path="src/main/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/test-classes" path="src/test/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
Added: ctakes/trunk/ctakes-constituency-parser-res/.project
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/.project?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/.project (added)
+++ ctakes/trunk/ctakes-constituency-parser-res/.project Tue Apr 2 17:41:30 2013
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>ctakes-constituency-parser-res</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.m2e.core.maven2Builder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ <nature>org.eclipse.m2e.core.maven2Nature</nature>
+ </natures>
+</projectDescription>
Added: ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.core.resources.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.core.resources.prefs (added)
+++ ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.core.resources.prefs Tue Apr 2 17:41:30 2013
@@ -0,0 +1,6 @@
+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
+encoding//src/test/java=UTF-8
+encoding//target/generated-sources/jcasgen=UTF-8
+encoding/<project>=UTF-8