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From	gandhira...@apache.org
Subject	svn commit: r1845321 [41/42] - in /ctakes/trunk/ctakes-web-rest: ./ src/ src/main/ src/main/java/ src/main/java/org/ src/main/java/org/apache/ src/main/java/org/apache/ctakes/ src/main/java/org/apache/ctakes/rest/ src/main/java/org/apache/ctakes/rest/f...
Date	Wed, 31 Oct 2018 11:04:01 GMT
Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/mitre/medfacts/uima/section_regex.xml URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/mitre/medfacts/uima/section_regex.xml?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/resources/org/mitre/medfacts/uima/section_regex.xml (added) +++ ctakes/trunk/ctakes-web-rest/src/main/resources/org/mitre/medfacts/uima/section_regex.xml Wed Oct 31 11:03:43 2018 @@ -0,0 +1,924 @@ +<?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\/\sreaction)?\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\shx\|habits)</expansion> + </fragment> +<!--MEDICATIONS--> + <fragment> + <name>medication1</name> + <expansion>(medications?\|medication\s$\ss\s$\|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> + <!-- fragments for subsections --> + <fragment> + <name>subsection-left</name> + <expansion>(\d+\.\s+\|\(\)?\|-(-)?\|\#(\#)?)</expansion> + </fragment> + <fragment> + <name>system</name> + <expansion>(\s+sys(\.\|tem)?)</expansion> + </fragment> + <fragment> + <name>conj</name> + <expansion>(\s,\s\|\s\&\s\|\s\/\s\|(\s,)?\s+and\s+)</expansion> + </fragment> + <fragment> + <name>sub</name> + <expansion>(\s\/\s\|\s--?\s\|\s+)</expansion> + </fragment> + <fragment> + <name>cardio</name> + <expansion>(cvs?\|cards?\|cardiac\|heart\|cardio(vascular(ly)?)?)</expansion> + </fragment> + <fragment> + <name>rhythm</name> + <expansion>((rate\s(\&\|\sand\s))?\srhythm\s((\&\|\sand\s)\srate)?)</expansion> + </fragment> + <fragment> + <name>pulmonary</name> + <expansion>(pulmo?\|pulmonary\|lungs\|chest\|respiratory\|resps?)</expansion> + </fragment> + <fragment> + <name>heme</name> + <expansion>(heme\|hematolog(y\|ic(ally)?))</expansion> + </fragment> + <fragment> + <name>lymph</name> + <expansion>(lymph(atic(s\|ally)?)?)</expansion> + </fragment> + +<!--ASSESSMENT/DISPOSITION/PLAN/INSTRUCTIONS--> +<!--IN-PATIENT COURSE--> +<!--DIAGNOSIS--> +<!--PROCEDURE/TREATMENT--> +</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\|\&\|\/)\splan)\|(?:a\s(?:\&\|\/)\sp))(<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;\sresponsible\s+after\s+study\s+for\s+causing\s+admission\s\)\s?))\s?)</regex> + <label>diagnoses</label> + </section> + <section> + <regex>((?:other\s+diagnosis\s;\sconditions\s\,\sinfections\s,\scomplications\s,\saffecting\s+treatment\s\/?\sstay)\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)?operative)\s+)?(?:problems\s+and\s+)?diagnos[ei]s(?:\s$\ses\s$)?)(<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\/\ssummary)(\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 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"/>)\sdata(<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\/\sprocedures)\|(?: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>((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\|pshx?)\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\|\&\|\/)\splan)\|(?: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\/\splans?))\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\/\sprocedures\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> +<subsections> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?General(ly)?\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>General</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Head\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>HEENT</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Eyes\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>HEENT</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Ears\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>HEENT</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Nose(<fragment-ref name="conj"/>Sinuses)?\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>HEENT</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Throat\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>HEENT</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?\b(HE)?ENT\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>HEENT</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Neck\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>Neck</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Throat<fragment-ref name="conj"/>Mouth<fragment-ref name="conj"/>Neck\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>Neck</label> <!-- or do we prefer HEENT here? --> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Neuro(logical(ly\|<fragment-ref name="system"/>)?)?\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>Neurological</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Nervous(<fragment-ref name="system"/>)?\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>Neurological</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)Psych(iatric)?\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>Psychiatric</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Abd(\.\|omen)?\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>Abdomen</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Breasts\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>Breasts</label> + </subsection> + <!-- CARDIOVASCULAR --> + <subsection> <!-- cardiovascular with or without "system" --> + <regex>((<fragment-ref name="subsection-left"/>)?<fragment-ref name="cardio"/>(<fragment-ref name="system"/>)?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Cardiovascular</label> + </subsection> + <subsection> <!-- cardiovascular rate & rhythm --> + <regex>((<fragment-ref name="subsection-left"/>)?<fragment-ref name="cardio"/><fragment-ref name="sub"/><fragment-ref name="rhythm"/>\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Cardiovascular</label> + </subsection> + <subsection> <!-- cardiovascular rhythm CV-R --> + <regex>((<fragment-ref name="subsection-left"/>)?CV\-R\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Cardiovascular</label> + </subsection> + <subsection> <!-- rate & rhythm alone --> + <regex>((<fragment-ref name="subsection-left"/>)?<fragment-ref name="rhythm"/>\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Cardiovascular</label> + </subsection> + <subsection> <!-- pump with or without cardio modifier --> + <regex>((<fragment-ref name="subsection-left"/>)?(<fragment-ref name="cardio"/><fragment-ref name="sub"/>)?pump\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Cardiovascular</label> + </subsection> + <subsection> <!-- COR (Cardiac Output Recorder) with or without cardio modifier --> + <regex>((<fragment-ref name="subsection-left"/>)?(<fragment-ref name="cardio"/><fragment-ref name="sub"/>)?COR\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Cardiovascular</label> + </subsection> + <subsection> <!-- cardiovascular pump CV-P --> + <regex>((<fragment-ref name="subsection-left"/>)?CV\-P\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Cardiovascular</label> + </subsection> + <subsection> <!-- coronary --> + <regex>((<fragment-ref name="subsection-left"/>)?Coronary\s\:)</regex> + <subsection_of>physical examination,review of systems</subsection_of> + <label>Cardiovascular</label> + </subsection> + <subsection> <!-- ischemia with or without cardio modifier --> + <regex>((<fragment-ref name="subsection-left"/>)?(<fragment-ref name="cardio"/><fragment-ref name="sub"/>)?ischemia\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Ischemia</label> + </subsection> + <subsection> <!-- cardiovascular ischemia --> + <regex>((<fragment-ref name="subsection-left"/>)?CV\-I\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Ischemia</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?(GI\|Gastro(intestinal)?)(<fragment-ref name="system"/>)?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Gastrointestinal</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?(GU\|(genito)?urinary)(<fragment-ref name="system"/>)?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Genitourinary</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Genital(s\|(<fragment-ref name="system"/>))?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Genitourinary</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?\bRenal(<fragment-ref name="system"/>)?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Genitourinary</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?(\bVasc(ular(ly\|<fragment-ref name="system"/>)?)?)\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Vascular</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?(Musculo)?skeletal(<fragment-ref name="system"/>)?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Musculoskeletal</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?(ID\|Infectious\s+Disease)\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Infectious Disease</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Endo(crine<fragment-ref name="system"/>?\|crinology)?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Endocrine</label> + </subsection> + <!-- Endocrine sub-subsections --> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Hyperthyroid\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Endocrine</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Hypothyroid\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Endocrine</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Diabetes\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Endocrine</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Adrenal\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Endocrine</label> + </subsection> + + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?(Ext(\.\|remities)?)\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Extremities</label> + </subsection> + <!-- include in pulmonary? + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Respiratory\s\:)</regex> + <subsection_of>physical examination</subsection_of> + <label>Respiratory</label> + </subsection> --> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?<fragment-ref name="pulmonary"/><fragment-ref name="system"/>?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Lungs</label> + </subsection> + <subsection> <!-- heme or lymph --> + <regex>((<fragment-ref name="subsection-left"/>)?(<fragment-ref name="heme"/>\|<fragment-ref name="lymph"/>)(<fragment-ref name="system"/>)?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Hematologic</label> + </subsection> + <subsection> <!-- heme and lymph --> + <regex>((<fragment-ref name="subsection-left"/>)?<fragment-ref name="heme"/><fragment-ref name="conj"/><fragment-ref name="lymph"/>(<fragment-ref name="system"/>s?)?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Hematologic</label> + </subsection> + <subsection> <!-- allergic or immmunologic (allergy/gies is reserved as main section head) --> + <regex>((<fragment-ref name="subsection-left"/>)?(All(ergic)?\|Immun(olog(y\|ic(ally)?))?)(<fragment-ref name="system"/>)?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Immunologic</label> + </subsection> + <subsection> <!-- allergic and immmunologic --> + <regex>((<fragment-ref name="subsection-left"/>)?All(ergic)?<fragment-ref name="conj"/>Immun(olog(y\|ic(ally)?))?(<fragment-ref name="system"/>s?)?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Immunologic</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Constitutional(ly)?(<fragment-ref name="system"/>)?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Constitutional</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Integumentar(il)?y(<fragment-ref name="system"/>)?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Integumentary</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Derma(tolog(ic(ally)?\|y))?(<fragment-ref name="system"/>)?\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Integumentary</label> + </subsection> + <subsection> <!-- tubes, lines, and drains --> + <regex>((<fragment-ref name="subsection-left"/>)?tubes<fragment-ref name="conj"/>lines<fragment-ref name="conj"/>drains\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Access</label> + </subsection> + <subsection> <!-- tubes/access or just access with optional dialysis modifier--> + <regex>((<fragment-ref name="subsection-left"/>)?(tubes<fragment-ref name="conj"/>)?(dialysis\s+)?access\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Access</label> + </subsection> + <subsection> <!-- (fluids, electrolytes and) mal/nutrition --> + <regex>((<fragment-ref name="subsection-left"/>)?(fluids<fragment-ref name="conj"/>electrolytes<fragment-ref name="conj"/>)?(mal)?nutrition\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Nutrition</label> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?FEN\s\:)</regex> + <subsection_of>physical examination,review of systems,hospital course</subsection_of> + <label>Nutrition</label> + </subsection> + </subsection> + <!-- subsections found in Hospital course only --> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?CC\s\:)</regex> + <subsection_of>hospital course</subsection_of> <!-- outside of hospital course, this could be carbon copy --> + <label>chief complaint</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Disp(o(sition)?)?\s\:)</regex> + <subsection_of>hospital course</subsection_of> + <label>disposition</label> + </subsection> + <subsection> + <regex>((<fragment-ref name="subsection-left"/>)?Proph(y(laxis)?)?\s\:)</regex> + <subsection_of>hospital course</subsection_of> + <label>prophylaxis</label> + </subsection> +</subsections> +<templates> + <template> + <regex>((.)\s\[\s\])</regex> + <label>false</label> + </template> + <template> + <regex>((.)\s\[\sx\s])</regex> + <label>true</label> + </template> +</templates> +</root> + Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak2 URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak2?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak2 (added) +++ ctakes/trunk/ctakes-web-rest/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak2 Wed Oct 31 11:03:43 2018 @@ -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\/\sreaction)?\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\shx\|habits)</expansion> + </fragment> +<!--MEDICATIONS--> + <fragment> + <name>medication1</name> + <expansion>(medications?\|medication\s$\ss\s$\|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\|\&\|\/)\splan)\|(?:a\s(?:\&\|\/)\sp))(<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;\sresponsible\s+after\s+study\s+for\s+causing\s+admission\s\)\s?))\s?)</regex> + <label>diagnoses</label> + </section> + <section> + <regex>((?:other\s+diagnosis\s;\sconditions\s\,\sinfections\s,\scomplications\s,\saffecting\s+treatment\s\/?\sstay)\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$\ses\s$)?)(<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\/\ssummary)(\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"/>)\sdata(<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\/\sprocedures)\|(?: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\|\&\|\/)\splan)\|(?: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\/\splans?))\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\/\sprocedures\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-web-rest/src/main/resources/pipers/AdvancedTokenizerPipeline.piper URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/AdvancedTokenizerPipeline.piper?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/AdvancedTokenizerPipeline.piper (added) +++ ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/AdvancedTokenizerPipeline.piper Wed Oct 31 11:03:43 2018 @@ -0,0 +1,24 @@ +// Commands and parameters to create a token processing pipeline with sections, paragraphs and lists + +// Annotate sections by known regex +add BsvRegexSectionizer + +// The sentence detector needs our custom model path, otherwise default values are used. +addLogged SentenceDetectorAnnotatorBIO classifierJarPath=/org/apache/ctakes/core/sentdetect/model.jar + +// The SentenceDetectorAnnotatorBIO is a "lumper" that works well for notes in which end of line does not indicate a sentence. +// If that is not your case, then you may get better results using the more standard SentenceDetector +// add SentenceDetector + +// By default, paragraphs are parsed using empty lines as separators and Part #: +add ParagraphAnnotator +// Fix sentences so that no sentence spans across two or more paragraphs. +add ParagraphSentenceFixer + +// Use regular expressions created for the Pitt notes to discover formatted lists and tables. +add ListAnnotator +// Fix sentences so that no sentence spans across two or more list entries. +add ListSentenceFixer + +// Now we can finally tokenize, tag parts of speech and chunk using adjusted sentences. +add TokenizerAnnotatorPTB Added: ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/AttributeCleartkSubPipe.piper URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/AttributeCleartkSubPipe.piper?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/AttributeCleartkSubPipe.piper (added) +++ ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/AttributeCleartkSubPipe.piper Wed Oct 31 11:03:43 2018 @@ -0,0 +1,19 @@ +// Commands and parameters to create a default entity attributes processing sub-pipeline. This is not a full pipeline. + +// Add the Dependency parser for use by cleartk +addDescription ClearNLPDependencyParserAE +// Add the Semantic Role Labeler parser for use by cleartk +addLogged ClearNLPSemanticRoleLabelerAE + +// Add the cleartk package for cleartk class lookups +package org.apache.ctakes.assertion.medfacts.cleartk + +// Add the cleartk attribute engines, logging for them as a block +add StartFinishLogger LOGGER_NAME=CleartkAnalysisEngine LOGGER_TASK="Assigning Attributes" IS_START=true +addDescription PolarityCleartkAnalysisEngine +addDescription UncertaintyCleartkAnalysisEngine +addDescription HistoryCleartkAnalysisEngine +addDescription ConditionalCleartkAnalysisEngine +addDescription GenericCleartkAnalysisEngine +addDescription SubjectCleartkAnalysisEngine +add StartFinishLogger LOGGER_NAME=CleartkAnalysisEngine LOGGER_TASK="Assigning Attributes" Added: ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/ChunkerSubPipe.piper URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/ChunkerSubPipe.piper?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/ChunkerSubPipe.piper (added) +++ ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/ChunkerSubPipe.piper Wed Oct 31 11:03:43 2018 @@ -0,0 +1,5 @@ +// Commands and parameters to create a default chunker processing sub-pipeline. This is not a full pipeline. + +add Chunker +addDescription adjuster.ChunkAdjuster NP,NP 1 +addDescription adjuster.ChunkAdjuster NP,PP,NP 2 Added: ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/CorefSubPipe.piper URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/CorefSubPipe.piper?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/CorefSubPipe.piper (added) +++ ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/CorefSubPipe.piper Wed Oct 31 11:03:43 2018 @@ -0,0 +1,10 @@ +// Commands and parameters to create a default coreference processing sub-pipeline. This is not a full pipeline. + +// A Dependency Parser is necessary, but is usually added for assertion so don't add one here + +// Constituency Parser adds Terminal Treebank Nodes, needed to create Markables +add ConstituencyParser + +add DeterministicMarkableAnnotator +addDescription MarkableSalienceAnnotator /org/apache/ctakes/temporal/ae/salience/model.jar +addDescription MentionClusterCoreferenceAnnotator /org/apache/ctakes/coreference/models/mention-cluster/model.jar Added: ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/Default.piper URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/Default.piper?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/Default.piper (added) +++ ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/Default.piper Wed Oct 31 11:03:43 2018 @@ -0,0 +1,20 @@ +// Commands and parameters to create a default plaintext document processing pipeline with UMLS lookup + +// set the thread count +threads 3 + +// Load a simple token processing pipeline from another pipeline file +load pipers/TsDefaultTokenizerPipeline + +// Add non-core annotators +add ContextDependentTokenizerAnnotator +addDescription POSTagger + +// Add Chunkers +load pipers/TsChunkerSubPipe + +// Default fast dictionary lookup +load pipers/TsDictionarySubPipe + +// Add Cleartk Entity Attribute annotators +load pipers/TsAttributeCleartkSubPipe Added: ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/DictionarySubPipe.piper URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/DictionarySubPipe.piper?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/DictionarySubPipe.piper (added) +++ ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/DictionarySubPipe.piper Wed Oct 31 11:03:43 2018 @@ -0,0 +1,10 @@ +// Commands and parameters to create a default dictionary lookup sub-pipeline. This is not a full pipeline. + +// path to the xml file containing information for dictionary lookup configuration. +cli LookupXml=org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml +// umls credentials +cli umlsUser=user +cli umlsPass=pass + +// Default fast dictionary lookup +add DefaultJCasTermAnnotator LookupXml=org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml Added: ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/Full.piper URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/Full.piper?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/Full.piper (added) +++ ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/Full.piper Wed Oct 31 11:03:43 2018 @@ -0,0 +1,17 @@ +// Advanced Tokenization: Regex sectionization, BIO Sentence Detector(lumper), Paragraphs,Lists +load pipers/AdvancedTokenizerPipeline.piper +add ContextDependentTokenizerAnnotator +add POSTagger +// Chunkers +load pipers/ChunkerSubPipe.piper +// Default fast dictionary lookup +load pipers/DictionarySubPipe.piper +add org.apache.ctakes.drugner.ae.DrugMentionAnnotator +// Cleartk Entity Attributes +load pipers/AttributeCleartkSubPipe.piper +// Temporal +load pipers/TemporalSubPipe.piper +// Coreferences +load pipers/CorefSubPipe.piper +add ContextAnnotator +add LabValueFinder \ No newline at end of file Added: ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TemporalSubPipe.piper URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TemporalSubPipe.piper?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TemporalSubPipe.piper (added) +++ ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TemporalSubPipe.piper Wed Oct 31 11:03:43 2018 @@ -0,0 +1,19 @@ +// Commands and parameters to create a default temporal processing sub-pipeline. This is not a full pipeline. + +// 'Generic' Events. Use addDescription and let the EventAnnotator set itself up with defaults. +addDescription EventAnnotator + +// Times. Use addLogged to log start and finish of processing. There aren't default models, so set specifically +addLogged BackwardsTimeAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/timeannotator/model.jar + +// DocTimeRel: the relation bin for Events to the Document Creation Time. +addLogged DocTimeRelAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/doctimerel/model.jar + +// Event - Time binary relations. +addLogged EventTimeRelationAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/eventtime/model.jar + +// Event - Event binary relations. +addLogged EventEventRelationAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/eventevent/model.jar + +// Need to improve. Generic Events (head words) should be replaced by overlapping subclasses with relations adjusted. +//add FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator Added: ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsAttributeCleartkSubPipe.piper URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsAttributeCleartkSubPipe.piper?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsAttributeCleartkSubPipe.piper (added) +++ ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsAttributeCleartkSubPipe.piper Wed Oct 31 11:03:43 2018 @@ -0,0 +1,19 @@ +// Commands and parameters to create a default entity attributes processing sub-pipeline. This is not a full pipeline. + +// Add the Dependency parser for use by cleartk +addDescription concurrent.ThreadSafeClearNlpDepParser +// Add the Semantic Role Labeler parser for use by cleartk +addDescription concurrent.ThreadSafeClearNlpSemRoleLabeler + +// Add the cleartk package for cleartk class lookups +package org.apache.ctakes.assertion.medfacts.cleartk + +// Add the cleartk attribute engines, logging for them as a block +add StartFinishLogger LOGGER_NAME=CleartkAnalysisEngine LOGGER_TASK="Assigning Attributes" IS_START=true +addDescription PolarityCleartkAnalysisEngine +addDescription UncertaintyCleartkAnalysisEngine +addDescription HistoryCleartkAnalysisEngine +addDescription ConditionalCleartkAnalysisEngine +addDescription GenericCleartkAnalysisEngine +addDescription SubjectCleartkAnalysisEngine +add StartFinishLogger LOGGER_NAME=CleartkAnalysisEngine LOGGER_TASK="Assigning Attributes" Added: ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsChunkerSubPipe.piper URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsChunkerSubPipe.piper?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsChunkerSubPipe.piper (added) +++ ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsChunkerSubPipe.piper Wed Oct 31 11:03:43 2018 @@ -0,0 +1,5 @@ +// Commands and parameters to create a default chunker processing sub-pipeline. This is not a full pipeline. + +add concurrent.ThreadSafeChunker +addDescription adjuster.ChunkAdjuster NP,NP 1 +addDescription adjuster.ChunkAdjuster NP,PP,NP 2 Added: ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsDefaultTokenizerPipeline.piper URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsDefaultTokenizerPipeline.piper?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsDefaultTokenizerPipeline.piper (added) +++ ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsDefaultTokenizerPipeline.piper Wed Oct 31 11:03:43 2018 @@ -0,0 +1,5 @@ +// Commands and parameters to create a default token processing pipeline + +add SimpleSegmentAnnotator +add concurrent.ThreadSafeSentenceDetector +add TokenizerAnnotatorPTB Added: ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsDictionarySubPipe.piper URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsDictionarySubPipe.piper?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsDictionarySubPipe.piper (added) +++ ctakes/trunk/ctakes-web-rest/src/main/resources/pipers/TsDictionarySubPipe.piper Wed Oct 31 11:03:43 2018 @@ -0,0 +1,10 @@ +// Commands and parameters to create a default dictionary lookup sub-pipeline. This is not a full pipeline. + +// path to the xml file containing information for dictionary lookup configuration. +cli LookupXml=l +// umls credentials +cli umlsUser=user +cli umlsPass=pass + +// Default fast dictionary lookup +add concurrent.ThreadSafeFastLookup LookupXml=org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml Added: ctakes/trunk/ctakes-web-rest/src/main/webapp/META-INF/MANIFEST.MF URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/webapp/META-INF/MANIFEST.MF?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/webapp/META-INF/MANIFEST.MF (added) +++ ctakes/trunk/ctakes-web-rest/src/main/webapp/META-INF/MANIFEST.MF Wed Oct 31 11:03:43 2018 @@ -0,0 +1,3 @@ +Manifest-Version: 1.0 +Class-Path: + Added: ctakes/trunk/ctakes-web-rest/src/main/webapp/WEB-INF/ctakes-rest-service-servlet.xml URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/webapp/WEB-INF/ctakes-rest-service-servlet.xml?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/webapp/WEB-INF/ctakes-rest-service-servlet.xml (added) +++ ctakes/trunk/ctakes-web-rest/src/main/webapp/WEB-INF/ctakes-rest-service-servlet.xml Wed Oct 31 11:03:43 2018 @@ -0,0 +1,16 @@ +<beans xmlns="http://www.springframework.org/schema/beans" + xmlns:context="http://www.springframework.org/schema/context" + xmlns:mvc="http://www.springframework.org/schema/mvc" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation=" http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-4.2.xsd http://www.springframework.org/schema/context + http://www.springframework.org/schema/context/spring-context-4.2.xsd http://www.springframework.org/schema/mvc http://www.springframework.org/schema/mvc/spring-mvc-4.2.xsd"> +<mvc:annotation-driven/> +<context:component-scan base-package="org.apache.ctakes.rest.service" /> + <mvc:cors> + <!-- allowed-origin can be set to specific valid URLs to tighten security --> + <mvc:mapping path="/service/" allowed-origins="" + allowed-methods="POST, GET, PUT, OPTIONS, DELETE" + allowed-headers="Content-Type,X-Requested-With,accept,Origin,Access-Control-Request-Method,Access-Control-Request-Headers,Authorization" + exposed-headers="Origin,Access-Control-Request-Method,Access-Control-Allow-Origin,Access-Control-Allow-Credentials" + allow-credentials="false"/> + </mvc:cors> +</beans> Added: ctakes/trunk/ctakes-web-rest/src/main/webapp/WEB-INF/web.xml URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/webapp/WEB-INF/web.xml?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/webapp/WEB-INF/web.xml (added) +++ ctakes/trunk/ctakes-web-rest/src/main/webapp/WEB-INF/web.xml Wed Oct 31 11:03:43 2018 @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<web-app version="2.5" xmlns="http://java.sun.com/xml/ns/javaee" +xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" +xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd"> + + <display-name>ctakes-rest-service</display-name> + <servlet> + <servlet-name>ctakes-rest-service</servlet-name> + <servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class> + <load-on-startup>0</load-on-startup> + </servlet> + <servlet-mapping> + <servlet-name>ctakes-rest-service</servlet-name> + <url-pattern>/service/</url-pattern> + </servlet-mapping> + <filter> + <filter-name>CORS</filter-name> + <filter-class>org.apache.ctakes.rest.filter.CORSFilter</filter-class> + </filter> + <filter-mapping> + <filter-name>CORS</filter-name> + <url-pattern>/service/</url-pattern> + </filter-mapping> +</web-app> Added: ctakes/trunk/ctakes-web-rest/src/main/webapp/index.jsp URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/webapp/index.jsp?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/webapp/index.jsp (added) +++ ctakes/trunk/ctakes-web-rest/src/main/webapp/index.jsp Wed Oct 31 11:03:43 2018 @@ -0,0 +1,19 @@ +<!DOCTYPE html> + +<html> + <head> + <link rel="stylesheet" type="text/css" href="css/index.css"> + <title> Ctakes Rest Service Test </title> + <script type="text/javascript" src="js/jquery.js"></script> + <script type="text/javascript" src="js/app.js"></script> + <script>var myContextPath = "${pageContext.request.contextPath}"</script> + </head> + <body> + <img src="http://ctakes.apache.org/images/ctakes_logo.jpg"/> + <br>Version: 4.0.1</br> + </br> + <h3>cTAKES REST SERVICE TESTING</h3> + <textarea id="analysisText" name="analysisText" rows="6" cols="75" onFocus="this.value=''">Enter your text for analysis</textarea><br> + <input type="button" value="Analyze" name="fire" id="fire"/> + </body> +</html> Added: ctakes/trunk/ctakes-web-rest/src/main/webapp/js/app.js URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/webapp/js/app.js?rev=1845321&view=auto ============================================================================== --- ctakes/trunk/ctakes-web-rest/src/main/webapp/js/app.js (added) +++ ctakes/trunk/ctakes-web-rest/src/main/webapp/js/app.js Wed Oct 31 11:03:43 2018 @@ -0,0 +1,23 @@ +$(document).ready(function() { + $('#fire').click(function() { + try { + $.ajax({ + url: myContextPath + "/service/analyze?pipeline=Default", + type: "POST", + crossDomain: true, + cache: false, + async: true, + data: document.getElementById("analysisText").value, + error: function(xhr, statusText, error) { + alert("Error processing REST call"); + }, + success: function(response, statusText, xhr) { + alert("Text analyzed successfully !!! Response JSON - " + JSON.stringify(response)); + } + }) + } catch (err) { + alert("Error invoking REST call - " + err.message); + } + + }); +});
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