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From seanfi...@apache.org
Subject svn commit: r1719760 [2/4] - in /ctakes/sandbox/dictionary-gui: data/ data/default/ data/optional/ data/small/ data/tim/ data/tiny/ lib/ src/main/java/org/apache/ctakes/dictionary/creator/gui/ctakes/ src/main/java/org/apache/ctakes/dictionary/creator/g...
Date Sun, 13 Dec 2015 04:27:44 GMT
Added: ctakes/sandbox/dictionary-gui/data/small/UnwantedSuffixes.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/small/UnwantedSuffixes.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/small/UnwantedSuffixes.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/small/UnwantedSuffixes.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,806 @@
+/
+'
+-
+- ( religious affiliation )
+- a specialty area of medicine
+- action
+- activity of daily living
+- assess ( & non urg )
+- attribute
+- biologic function
+- category
+- confectionery
+- dietary
+- entertainment ( & [ musical ]
+- finding
+- function
+- general -
+- herbal supplement
+- mental defense mechanism
+- mental process
+- observation
+- organization
+- physical agent
+- related finding
+- rolecode
+- speciality
+- specialty
+- summary
+- symptom
+- weather
+- sport
+( a priority lower than stat )
+( abnormality )
+( abo blood group )
+( acholeplasma host )
+( acknowledgementcondition )
+( acquired )
+( action )
+( action )
+( activated )
+( activity )
+( activity )
+( actual )
+( adjudicators ( & top )
+( adl finding )
+( administative )
+( administration method )
+( administrative concept )
+( age group )
+( alcohol )
+( all components )
+( all fractions of )
+( allelic variant )
+( alone )
+( alphabetic group )
+( alternative )
+( amount )
+( amphibian )
+( anatomical classification )
+( anatomical coordinate )
+( anatomical descriptor )
+( anatomical feature )
+( anatomical location )
+( anatomy )
+( and accessories )
+( and related agents )
+( angiosperm hosts )
+( animal )
+( any part )
+( apparatus )
+( applies to non-numeric results )
+( area of increased mortality )
+( area of knowledge )
+( arrangement )
+( art )
+( artificial )
+( artistic )
+( ascomycota )
+( assessment )
+( assessment scale )
+( astronomy )
+( at present )
+( attitude )
+( attribute )
+( attributes )
+( audit )
+( australia )
+( available ( qualifier ) )
+( bacteria )
+( bacteria and cyanobacteria hosts )
+( battery - powered )
+( beach )
+( beach , court )
+( beet sugar )
+( behavior )
+( behavior finding )
+( beverage )
+( biologic function )
+( biological )
+( biological function )
+( biological funtion )
+( biopsy result )
+( bird )
+( blacus )
+( blood components )
+( blood pressure )
+( body part )
+( body structure )
+( body substance )
+( botanical taxonomic category below variety )
+( brain )
+( brain structure )
+( button )
+( calcified structure )
+( canal )
+( cancer stage )
+( candy )
+( cardiac conduction )
+( category )
+( catering and lodging services )
+( cell )
+( cell line )
+( cell structure )
+( cells or organisms )
+( central nervous system tumor )
+( central nervous system tumour )
+( cerebellum )
+( certification )
+( change )
+( characteristic )
+( chemical )
+( chemical / related processes )
+( chemical and related processes )
+( chemical processes , except petroleum )
+( citrus )
+( class )
+( classical )
+( classification )
+( cleansing action )
+( clinical )
+( clinical definition )
+( clinical disorder )
+( clinical specialty )
+( color )
+( combined site )
+( comfort level finding )
+( communication )
+( communicationfunctiontype )
+( community )
+( company )
+( compartment )
+( complement activation )
+( complete ) ( partial )
+( component )
+( composite )
+( compression algorithm )
+( computer )
+( computer files directory )
+( computer network )
+( concept )
+( construction )
+( container status )
+( containing tobacco )
+( context - dependent category )
+( contextual qualifier )
+( copy in notes )
+( copy within chart )
+( court )
+( crustacea )
+( crustacean )
+( data - processing )
+( data )
+( data type )
+( dataset )
+( dedicated instruments )
+( degree / certification )
+( degree / license / certification )
+( dental procedure )
+( detection and tagging )
+( deviation )
+( device )
+( device status )
+( diagnosis )
+( diagnostic , surgical , and therapeutic interventions )
+( dicotyledons hosts )
+( dietary )
+( digestive structure of animal )
+( diminutive )
+( direction )
+( discharge )
+( discipline )
+( disease )
+( disease attribute )
+( diskus intervertebralis )
+( disorder )
+( do as near as possible to requested time )
+( do immediately )
+( document )
+( document type )
+( documents )
+( dry - cleaner )
+( dysfunction )
+( economic )
+( economic descriptor )
+( economic status )
+( edible )
+( edible oils )
+( education )
+( electric power )
+( electrical )
+( embryology )
+( embryonic structure )
+( emergency )
+( emotion )
+( emotional response )
+( end postition )
+( england & wales )
+( england and wales )
+( entertainment )
+( entire collection )
+( entity )
+( environment )
+( environmental process )
+( epidemiology )
+( equipment )
+( ethnic group )
+( eukaryote )
+( event )
+( event history )
+( except advertising )
+( except aircraft and marine engines )
+( except aircraft and marine turbines )
+( except construction )
+( except electrical )
+( except lawyer or judge )
+( except motor vehicle )
+( except oil and gas wells )
+( except photo - gravers )
+( except rubber )
+( except ships ' engines )
+( except tire maker / tire vulcanizer )
+( except tire makers and tire vulcanisers )
+( except tire makers and tire vulcanizers )
+( except transport )
+( experimental )
+( experimental system )
+( exposure / injury )
+( extensiveness )
+( external anatomical feature )
+( eye )
+( family )
+( family issue )
+( female )
+( field )
+( fiinding )
+( film )
+( films )
+( finding )
+( findings )
+( fish )
+( flies )
+( flower )
+( follower of religion - person )
+( food )
+( for any age )
+( for cleaning purpose )
+( for gunter ' s chain )
+( for pain relief )
+( for staff )
+( for transmitting doses for pharmacokinetics )
+( formal meetings )
+( formation )
+( foundry )
+( freight train )
+( frequency )
+( fruit )
+( function )
+( function )
+( fungi hosts )
+( fungus )
+( garment )
+( gauge size )
+( general )
+( generic version )
+( genetics )
+( genu )
+( geographic )
+( geographic area )
+( geographic location )
+( glandula suprarenalis )
+( goal )
+( grade )
+( gramineae hosts )
+( grooming )
+( grooming )
+( group )
+( group of parts )
+( guideline )
+( gunter ' s chain )
+( hand - operated machine )
+( heading )
+( health )
+( health care )
+( healthcare )
+( helper cells )
+( hemorrhage )
+( high voltage )
+( histology )
+( history )
+( horizontal architectural support )
+( horse )
+( hosiery )
+( human only )
+( hypothalamus )
+( i . q . . . . . )
+( iadl finding )
+( idea )
+( identifier )
+( image )
+( in-store merchandise )
+( in animal tissues )
+( in vivo )
+( including digits )
+( indicator )
+( infection )
+( injury )
+( input )
+( inquiry )
+( insect )
+( insect hosts )
+( instep )
+( instruction )
+( instruction imperative )
+( intake )
+( interactions )
+( intercourse )
+( invertebrate )
+( island )
+( january 2007 release )
+( kind of quantity )
+( lab finding )
+( lab procedure )
+( lab result )
+( lab technique )
+( lab test )
+( laboratory finding )
+( laboratory procedure )
+( land - based )
+( laparotomy performed )
+( length )
+( lepidoptora hosts )
+( libraries )
+( libraries )
+( life event - finding )
+( life style )
+( line - film )
+( lingual , palatine , pharyngeal )
+( link assertion )
+( linkage concept )
+( liquid )
+( list bullets )
+( list separately in addition to code for primary procedure )
+( living organism )
+( location )
+( logging )
+( long - distance transport )
+( lower case a )
+( machine )
+( machine , except jacquard loom )
+( machines )
+( male )
+( malting )
+( mammal )
+( mapping )
+( marine pseudomonad hosts )
+( masonry and woodwork )
+( material )
+( mating )
+( measurement )
+( medical device )
+( medically )
+( medium of exchange )
+( medulla )
+( medullae )
+( medullary reticular formation )
+( member of religious order )
+( membrane )
+( mental function )
+( mental process )
+( metabolim test )
+( metal )
+( metal melting , except cupola )
+( metal reheating )
+( method )
+( military )
+( mine )
+( mine / quarry )
+( mine and quarry )
+( minor structure )
+( miscellaneous )
+( modified )
+( modifier )
+( molecular function )
+( molecular structure )
+( morphologic abnormality )
+( morphologic abnormality , calcified structure )
+( morphology )
+( motion )
+( motion picture )
+( motivation )
+( musical )
+( nanoparticle )
+( natural and artificial )
+( nature of procedure values )
+( navigational concept )
+( neck )
+( nmo )
+( non-ferrous metals )
+( non medication )
+( nonoperative )
+( not alarm reaction )
+( number )
+( numerical qualifier )
+( object )
+( observable )
+( observable entity )
+( observation )
+( observation or disorder )
+( occasion for eating )
+( occupation )
+( occupation history )
+( occupation or discipline )
+( occupational group )
+( ocular )
+( oil / gas wells )
+( oil and gas wells )
+( oilfield )
+( oils and fats )
+( old people ' s home )
+( operative )
+( or )
+( oral challenge )
+( ore smelting )
+( organ )
+( organ component )
+( organ part )
+( organisation )
+( organism )
+( organization )
+( origin )
+( origins )
+( orthodontic procedure )
+( other )
+( output )
+( package insert )
+( pairs )
+( pairs )
+( palatine )
+( parameter )
+( part organ )
+( patient )
+( patient instructions )
+( pdq )
+( per time )
+( per volume )
+( person )
+( personality )
+( persons )
+( pertaining to a node )
+( petroleum refining )
+( phenomenon )
+( philosophy )
+( physical activity )
+( physical activity )
+( physical device )
+( physical finding )
+( physical force )
+( physical force )
+( physical geography )
+( physical object )
+( physical object )
+( physician )
+( physician group )
+( physiologic )
+( physiologic function )
+( physiology )
+( planet )
+( plant )
+( plant hosts )
+( plant part )
+( plants hosts )
+( platelet )
+( polypectomy )
+( population )
+( population )
+( population group )
+( position )
+( postinfection )
+( postoperative )
+( potency unit )
+( power station )
+( ppc - c )
+( prescription )
+( present illness )
+( present time )
+( press / radio / t . v . )
+( primary )
+( primary procedure )
+( printing )
+( private service )
+( procedure )
+( procedure detail )
+( procedure or disorder )
+( process )
+( process of discrimination )
+( product )
+( profession )
+( property )
+( property of measurement )
+( prosthesis )
+( protons , ions )
+( protozoa )
+( provider role )
+( psychiatric )
+( psychiatry )
+( psychologic )
+( psychological function )
+( psychology )
+( psychophysiology )
+( psychotherapy )
+( publication )
+( publication format )
+( publications )
+( pure mathematics )
+( qualifier )
+( qualifier in lnc )
+( qualifier value )
+( qualifier value )
+( quality )
+( race )
+( racial group )
+( radio / t . v . )
+( radio / television )
+( radio / television / radar equipment )
+( radio broadcasts )
+( radioactive materials )
+( radiologist )
+( rate )
+( reassigned )
+( record )
+( record artifact )
+( recreational activity )
+( reference documentation )
+( regime / therapy )
+( region )
+( region of foot )
+( rehabilitation )
+( reimbursement )
+( relative )
+( religion )
+( religion / philosophy )
+( reptile )
+( respiratory measure )
+( response modality )
+( result )
+( revised )
+( rifle )
+( road )
+( role )
+( rolling mill )
+( route )
+( route of administration )
+( schedule frequency )
+( science )
+( scotland )
+( sea )
+( season )
+( second level )
+( section of report )
+( self - care status )
+( sensation )
+( separate procedure )
+( serotype )
+( serous membrane )
+( services standards )
+( set of actions )
+( severe )
+( severity modifier )
+( shape )
+( shin )
+( ship )
+( singles )
+( site )
+( site of care )
+( situation )
+( sleep disorder )
+( slowed )
+( small pieces )
+( snails )
+( social behavior )
+( social concept )
+( social status )
+( sound )
+( sound intensity )
+( source type )
+( spatial )
+( special concept )
+( specialised )
+( specialized )
+( specialty )
+( specific stage )
+( specify )
+( specify level )
+( specify type )
+( specimen )
+( specimen source code )
+( spice )
+( sport )
+( sports activity )
+( stage / studio )
+( stage and studio )
+( staging scale )
+( statement )
+( statistical )
+( statistical adjustment )
+( statistical procedure )
+( statistical technique )
+( status )
+( steam )
+( steel )
+( steel converting )
+( steel refining )
+( still camera )
+( strain )
+( structure )
+( subdivision )
+( substance )
+( substance / material )
+( substance status )
+( substantia innominata )
+( substitution condition )
+( suffix )
+( sugar refining )
+( suppressor cells )
+( surface )
+( surface region )
+( surface region of back )
+( surgical )
+( surgical procedure )
+( surgical speciality )
+( surgical view )
+( symbol )
+( symptom )
+( system )
+( taxon )
+( technician / technologist )
+( techniques )
+( temporal )
+( temporal concept )
+( temporal qualifier )
+( terminology entity )
+( test result )
+( testicles )
+( theater )
+( theatre )
+( theoretical )
+( therapeutic )
+( therapy )
+( therapy ) ( diagnostic id )
+( third level )
+( time frame )
+( time pattern )
+( time period )
+( time point or interval )
+( tissue )
+( tissue integrity )
+( to be done prior to surgery )
+( traffic )
+( transanal disk excision )
+( transmission )
+( transportation )
+( treatment )
+( trust territory )
+( tumor staging )
+( type )
+( type of material , substance )
+( u . s . )
+( uniformity )
+( unit )
+( unit of mass )
+( unit of measure )
+( unit of pressure )
+( unmodified )
+( upper )
+( us )
+( use calc )
+( use of drug )
+( use only with codes for immunization )
+( used to identify procedures performed on the left side of the body )
+( used to identify procedures performed on the right side of the body )
+( uterine )
+( value )
+( variant )
+( vegetable )
+( version 4 )
+( vertebral column )
+( vertebrale )
+( vocalization )
+( volume )
+( wait and see )
+( wasp )
+( waterworks )
+( weight )
+( wood distillation )
+( workshop )
+( yes / no )
+( zoology )
+,
+, cs
+, device
+, disorder
+, follower of religion
+, function
+, life event
+, services & procedure codes ( category iii , temporary )
+, united states
+[ any part ]
+[ a body part ]
+[ action ]
+[ activity ]
+[ adjective ]
+[ an instruction material ]
+[ any part ]
+[ artwork ]
+[ ball ]
+[ body ]
+[ body function ]
+[ body part ]
+[ body parts ]
+[ character ]
+[ chemical / ingredient ]
+[ clothing ]
+[ color ]
+[ device ]
+[ disease / finding ]
+[ document ]
+[ dose form ]
+[ economics ]
+[ environment ]
+[ executive duty ]
+[ extent ]
+[ finding ]
+[ fish ]
+[ follower of religion ]
+[ for organism ( & culture ) ]
+[ furniture ]
+[ game ]
+[ garment ]
+[ hiv ]
+[ in an environmental context ]
+[ in social context ]
+[ mammal ]
+[ manufactured object ]
+[ manufactured product ]
+[ mating posture ]
+[ medical device ]
+[ mental function ]
+[ mental process ]
+[ moa ]
+[ molecular function ]
+[ money ]
+[ motion ]
+[ ngu ]
+[ object ]
+[ occupation ]
+[ organism ] or [ infection - shingles ]
+[ organization ]
+[ paper report ]
+[ pe ]
+[ people ]
+[ physical phenomenon ]
+[ plan ]
+[ plant ]
+[ procedure ]
+[ product ]
+[ profession ]
+[ psychology ]
+[ publication type ]
+[ race ]
+[ reference materials ]
+[ room ]
+[ sample ]
+[ specialty ]
+[ sports ]
+[ statistical concept ]
+[ status ]
+[ substance ]
+[ surgical action ]
+[ uniformity ]
+[ unit of measurement ]
+[ unit of pressure ]
+] ( person )
+{ organization ]
+< subjective >
+epidemiology
+status ( & consent )

Added: ctakes/sandbox/dictionary-gui/data/tim/ConversionSources.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tim/ConversionSources.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tim/ConversionSources.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tim/ConversionSources.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,4 @@
+ICD10PCS
+ICD9CM
+RXNORM
+SNOMEDCT

Added: ctakes/sandbox/dictionary-gui/data/tim/ModifierSuffixes.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tim/ModifierSuffixes.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tim/ModifierSuffixes.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tim/ModifierSuffixes.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1 @@
+// Don't automatically modify for small

Added: ctakes/sandbox/dictionary-gui/data/tim/RemovalColonTriggers.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tim/RemovalColonTriggers.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tim/RemovalColonTriggers.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tim/RemovalColonTriggers.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,38 @@
+: - :
+: 24 hours :
+: 8 hours :
+: address :
+: arbitrary concentration :
+: duration of encounter :
+: duration of the study :
+: finding :
+: identifier :
+: impression / interpretation of study :
+: life of the unit :
+: mass :
+: number :
+: point in time :
+: prid :
+: pt :
+: substance concentration :
+: text :
+: type :
+: volume :
+: volume rate :
+// The following are in UnwantedSuffixes for default, but trigger removal for small
+:
+: - -
+: - : point in time : ^ patient : - : phenx
+: ( & glucose ( & plasma ) )
+: ( & nos )
+: [ & named variants ]
+: [ admin ] or [ exam ]
+: [ drivers exam ] or [ dtp20003 - hgv / publ serv claim ] or [ admin ]
+: [ early morning ] or [ mid-stream ] or [ for organism ( & culture ) ]
+: [ exam ( & admin ) ] ) or [ my22 form ]
+: [ fp78 ] or [ gp78 ]
+: [ implantation ] or [ implant ]
+: [ monitoring ] or [ clinic ]
+: [ nos ]
+: [ officer ] or [ executive ]
+: [ production ] or [ product ]

Added: ctakes/sandbox/dictionary-gui/data/tim/RemovalFunctionTriggers.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tim/RemovalFunctionTriggers.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tim/RemovalFunctionTriggers.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tim/RemovalFunctionTriggers.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,4 @@
+] or [
+] & / or [
+) or (
+) & / or (
\ No newline at end of file

Added: ctakes/sandbox/dictionary-gui/data/tim/RemovalPrefixTriggers.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tim/RemovalPrefixTriggers.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tim/RemovalPrefixTriggers.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tim/RemovalPrefixTriggers.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,32 @@
+deprecated 
+retired procedure
+// The following are in UnwantedPrefixes for the default, but here for small
+[ d ]
+[ edta ]
+[ m ]
+[ q ]
+[ v ]
+[ x ]
+[ so ]
+// activities involving
+and unspecified
+( non-specific )
+child :
+college of american pathologists cancer checklist ;
+// other activity involving
+other
+phenx -
+specimen source code -
+specimen source codes -
+specimen source codes =
+ or
+#
+&
+& [
+'
+*
+-
+:
+?
+
+

Added: ctakes/sandbox/dictionary-gui/data/tim/RemovalSuffixTriggers.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tim/RemovalSuffixTriggers.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tim/RemovalSuffixTriggers.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tim/RemovalSuffixTriggers.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,249 @@
+- retired code
+- retired -
+- retired
+( reassigned )
+[ obsolete ]
+( deprecated )
+// The following are in UnwantedSuffixes for default, but trigger removal for small
+- ( other )
+- duplicate -
+- nos
+- retired
+- retired -
+- unspec
+- unspecified
+ as topic
+ as topics
+ nec
+ nec in snomedct
+ nos
+ not otherwise specified
+ or
+ title 18
+( or )
+( 10 )
+( _ _ _ 0 , 2 )
+( deprecated )
+( except leather and fur )
+( hl7v3 . 0 concept )
+( inactive concept )
+( mesh category )
+( namespace concept )
+( non-specific )
+( nos )
+( not elsewhere classified in lnc )
+( obsolete notation )
+( procedure nec )
+( process of differentiation )
+) ( adjudicators ( & top )
+& / or o / e
+& / or orderly ( & [ orderlies ] )
+& [ fistula ]
+& [ symptom ]
+& [ legal ]
+& [ symptom ]
+& [ vehicle ]
+( & [ reimbursement ] )
+( & [ abnormal ] )
+( & [ acquired ] )
+( & [ acute ] )
+( & [ acute nos ] )
+( & [ broad ligament ] )
+( & [ bupa examination done ] )
+( & [ c / o - ] )
+( & [ c / o ] )
+( & [ chart ] )
+( & [ duct ] or [ gland ] )
+( & [ eating observation ] )
+( & [ etc ] )
+( & [ expiratory ] )
+( & [ eye disorder ] )
+( & [ government ] )
+( & [ hall ] )
+( & [ infection ] )
+( & [ keen ] )
+( & [ labor complicated by ] )
+( & [ laborer nos ] )
+( & [ labour complicated by ] )
+( & [ labourer nos ] )
+( & [ machine ] and / or [ press ] )
+( & [ member of phct ] )
+( & [ miners ( & coal )
+( & [ named variants ] )
+( & [ nec ] )
+( & [ nos ] )
+( & [ obstructive ] )
+( & [ occupation ] )
+( & [ occupations ] )
+( & [ officer ] )
+( & [ product ] )
+( & [ refer ] )
+( & [ referral ] )
+( & [ referral to ] )
+( & [ reimbursement ] )
+( & [ retail ] )
+( & [ rubber ] )
+( & [ staff ] )
+( & [ staghorn ] )
+( & [ symptom ] )
+( & [ teachers ] )
+( & [ unmarried ] )
+( & [ unspecified ] )
+( & [ warfarin ] )
+( & [ weightlessness ] )
+( & [ well ] )
+( & acquired )
+( & acute )
+( & admin )
+( & administration )
+( & ankle joint )
+( & assess )
+( & attic )
+( & bladder )
+( & blind )
+( & c / o )
+( & c / s )
+( & certificate )
+( & chronic )
+( & claim )
+( & claim gp / ms )
+( & congenital )
+( & conjunctiva )
+( & consent )
+( & dialysis )
+( & direct )
+( & disorder )
+( & distal )
+( & drug )
+( & expiratory )
+( & f303 )
+( & floor / wall )
+( & food poison )
+( & form )
+( & form gp45 ) )
+( & form : [ fp70a ] or [ gp / pea ] )
+( & from patient )
+( & held )
+( & hepatic duct )
+( & in blood )
+( & infection )
+( & infestation )
+( & level ( & phenylalanine ) )
+( & level )
+( & localization )
+( & marital )
+( & maternity allowances )
+( & mobile unit x-ray )
+( & named variants )
+( & nec )
+( & non urg )
+( & nos )
+( & o / e )
+( & on medical advice )
+( & operation )
+( & other )
+( & pathology )
+( & patient data )
+( & peritonsillar region )
+( & pleural )
+( & provision )
+( & record )
+( & referred to )
+( & report )
+( & result )
+( & sample )
+( & sc1 - given to staff )
+( & scrotal skin )
+( & short hip rotator )
+( & sinus )
+( & skin )
+( & skin of external ear )
+( & skin of external nose )
+( & skin of eyebrow )
+( & skin of eyelid )
+( & skin of male perineum )
+( & skin of nipple )
+( & skin of penis )
+( & skin of vulva )
+( & stock order gp10a )
+( & swab )
+( & symptom )
+( & tanner )
+( & top )
+( & top managers )
+( & traumatic )
+( & umbilical skin )
+( & unspecified )
+( & upper )
+( & vaccination )
+( & various types )
+( & viral )
+( & with stabilisation )
+( & with stabilization )
+( * )
+( _ _ _ per hpf )
+( + / - religion )
+( = breath )
+( = breath )
+( = stone )
+( = stone )
+[ & aircraft ]
+[ & bacterial ]
+[ & glucose ]
+[ & named variants ]
+[ & nos ]
+[ & professional ]
+[ & symptom ]
+[ ambiguous ]
+[ dup ]
+[ duplicate ]
+[ obsolete ]
+[ other ]
+, nec in snomedct
+, nos
+, not elsewhere classified
+, unclassified
+, unspecified
+, unspecified part
+concept ( inactive concept )
+reason not stated ( inactive concept )
+// New for tiny
+&
+: phenx
+// Added for form cleanup 11/3/2014 spf
+( # _ _ _ )
+( / _ _ _ )
+( _ _ _ / )
+( j _ _ _ )
+( _ _ _ 0 , 2 )
+( _ _ _ 0 - 30 )
+( _ _ _ bpm )
+( _ _ _ cm )
+( _ _ _ _ cm )
+( _ _ _ _ _ cm )
+( _ _ _ cm2 )
+( _ _ _ degrees )
+( _ _ _ m2 )
+( _ _ _ mets )
+( _ _ _ min )
+( _ _ _ minutes each time )
+( _ _ _ per hpf )
+( minus _ _ _ )
+( _ _ _ ml / hr )
+( _ _ _ ml per second )
+( plus _ _ _ )
+( _ _ _ sec )
+: plus _ _ _
+_ _ _ %
+_ _ _ cm
+add _ _ _
+// Added for Tim Other
+( sensu insecta )
+( sensu drosophila )
+ 500 ml
+& / or fluid
+}
+[ 1 ]
+[ 2 ]
+[ 3 ]
+[ 4 ]

Added: ctakes/sandbox/dictionary-gui/data/tim/RightAbbreviations.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tim/RightAbbreviations.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tim/RightAbbreviations.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tim/RightAbbreviations.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,8 @@
+// No automatic abbreviation extraction for tim, but some synonyms
+( possession )
+( rush against )
+( release )
+( better )
+( obedience )
+( alcohol or other drugs )
+( beliefs )

Added: ctakes/sandbox/dictionary-gui/data/tim/TimDrugTuis.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tim/TimDrugTuis.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tim/TimDrugTuis.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tim/TimDrugTuis.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1 @@
+// No desired "true" drug tuis

Added: ctakes/sandbox/dictionary-gui/data/tim/TimNonDrugSources.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tim/TimNonDrugSources.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tim/TimNonDrugSources.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tim/TimNonDrugSources.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,55 @@
+AIR
+AOD
+AOT
+CCS
+CHV
+COSTAR
+CSP
+CST
+DXP
+FMA
+GO
+HCPCS
+HL7V2.5
+HL7V3.0
+HUGO
+ICD10PCS
+ICD9CM
+ICPC
+ICPCBAQ
+ICPCDAN
+ICPCDUT
+ICPCFIN
+ICPCFRE
+ICPCGER
+ICPCHEB
+ICPCHUN
+ICPCITA
+ICPCNOR
+ICPCPOR
+ICPCSPA
+ICPCSWE
+LCH
+LNC
+MCM
+MEDLINEPLUS
+MSH
+MTH
+MTHCH
+MTHHH
+MTHHL7V2.5
+MTHICD9
+MTHMST
+MTHMSTFRE
+MTHMSTITA
+NCBI
+OMIM
+PDQ
+QMR
+RAM
+SNOMEDCT
+SPN
+SRC
+TKMT
+USPMG
+UWDA

Added: ctakes/sandbox/dictionary-gui/data/tim/TimOtherTuis.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tim/TimOtherTuis.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tim/TimOtherTuis.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tim/TimOtherTuis.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,33 @@
+// ACTI Activities & Behaviors
+T051
+T052
+T053
+T054
+T055
+T056
+T057
+T064
+T066
+// DEVI Devices
+// 74 is medical device OBJ
+T074
+// 75 is research device OBJ
+T075
+// 203 is drug delivery OBJ  -  but has too many drugs and amounts
+// T203
+// OBJC Objects
+T167
+T168
+T071
+T072
+T073
+// OCCU Occupations
+T090
+T091
+// PROC Procedures
+// 58 is health care ACTI, not covered by cTakes
+T058
+// 62 is research ACTI, not covered by cTakes
+T062
+// 65 is educational ACTI, not covered by cTakes
+T065

Added: ctakes/sandbox/dictionary-gui/data/tim/TimSpecificTuis.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tim/TimSpecificTuis.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tim/TimSpecificTuis.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tim/TimSpecificTuis.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,19 @@
+// ACTI Activities & Behaviors
+T051
+T052
+T053
+T054
+T055
+T056
+T057
+T064
+T066
+// OBJC Objects
+T167
+T168
+T071
+T072
+T073
+// OCCU Occupations
+T090
+T091

Added: ctakes/sandbox/dictionary-gui/data/tim/UnwantedPrefixes.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tim/UnwantedPrefixes.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tim/UnwantedPrefixes.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tim/UnwantedPrefixes.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,3 @@
+( congenital )
+engaged in
+entire 

Added: ctakes/sandbox/dictionary-gui/data/tim/UnwantedSuffixes.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tim/UnwantedSuffixes.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tim/UnwantedSuffixes.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tim/UnwantedSuffixes.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,902 @@
+/
+'
+-
+- ( religious affiliation )
+- a specialty area of medicine
+- action
+- activity of daily living
+- assess ( & non urg )
+- attribute
+- biologic function
+- category
+- confectionery
+- dietary
+- entertainment ( & [ musical ]
+- finding
+- function
+- general -
+- herbal supplement
+- mental defense mechanism
+- mental process
+- observation
+- organization
+- physical agent
+- related finding
+- rolecode
+- speciality
+- specialty
+- summary
+- symptom
+- weather
+- sport
+( a priority lower than stat )
+( abnormality )
+( abo blood group )
+( acholeplasma host )
+( acknowledgementcondition )
+( acquired )
+( action )
+( action )
+( activated )
+( activity )
+( activity )
+( actual )
+( adjudicators ( & top )
+( adl finding )
+( administative )
+( administration method )
+( administrative concept )
+( age group )
+( alcohol )
+( all components )
+( all fractions of )
+( allelic variant )
+( alone )
+( alphabetic group )
+( alternative )
+( amount )
+( amphibian )
+( anatomical classification )
+( anatomical coordinate )
+( anatomical descriptor )
+( anatomical feature )
+( anatomical location )
+( anatomy )
+( and accessories )
+( and related agents )
+( angiosperm hosts )
+( animal )
+( any part )
+( apparatus )
+( applies to non-numeric results )
+( area of increased mortality )
+( area of knowledge )
+( arrangement )
+( art )
+( artificial )
+( artistic )
+( ascomycota )
+( assessment )
+( assessment scale )
+( astronomy )
+( at present )
+( attitude )
+( attribute )
+( attributes )
+( audit )
+( australia )
+( available ( qualifier ) )
+( bacteria )
+( bacteria and cyanobacteria hosts )
+( battery - powered )
+( beach )
+( beach , court )
+( beet sugar )
+( behavior )
+( behavior finding )
+( beverage )
+( biologic function )
+( biological )
+( biological function )
+( biological funtion )
+( biopsy result )
+( bird )
+( blacus )
+( blood components )
+( blood pressure )
+( body part )
+( body structure )
+( body substance )
+( botanical taxonomic category below variety )
+( brain )
+( brain structure )
+( button )
+( calcified structure )
+( canal )
+( cancer stage )
+( candy )
+( cardiac conduction )
+( category )
+( catering and lodging services )
+( cell )
+( cell line )
+( cell structure )
+( cells or organisms )
+( central nervous system tumor )
+( central nervous system tumour )
+( cerebellum )
+( certification )
+( change )
+( characteristic )
+( chemical )
+( chemical / related processes )
+( chemical and related processes )
+( chemical processes , except petroleum )
+( citrus )
+( class )
+( classical )
+( classification )
+( cleansing action )
+( clinical )
+( clinical definition )
+( clinical disorder )
+( clinical specialty )
+( color )
+( combined site )
+( comfort level finding )
+( communication )
+( communicationfunctiontype )
+( community )
+( company )
+( compartment )
+( complement activation )
+( complete ) ( partial )
+( component )
+( composite )
+( compression algorithm )
+( computer )
+( computer files directory )
+( computer network )
+( concept )
+( construction )
+( container status )
+( containing tobacco )
+( context - dependent category )
+( contextual qualifier )
+( copy in notes )
+( copy within chart )
+( court )
+( crustacea )
+( crustacean )
+( data - processing )
+( data )
+( data type )
+( dataset )
+( dedicated instruments )
+( degree / certification )
+( degree / license / certification )
+( dental procedure )
+( detection and tagging )
+( deviation )
+( device )
+( device status )
+( diagnosis )
+( diagnostic , surgical , and therapeutic interventions )
+( dicotyledons hosts )
+( dietary )
+( digestive structure of animal )
+( diminutive )
+( direction )
+( discharge )
+( discipline )
+( disease )
+( disease attribute )
+( diskus intervertebralis )
+( disorder )
+( do as near as possible to requested time )
+( do immediately )
+( document )
+( document type )
+( documents )
+( dry - cleaner )
+( dysfunction )
+( economic )
+( economic descriptor )
+( economic status )
+( edible )
+( edible oils )
+( education )
+( electric power )
+( electrical )
+( embryology )
+( embryonic structure )
+( emergency )
+( emotion )
+( emotional response )
+( end postition )
+( england & wales )
+( england and wales )
+( entertainment )
+( entire collection )
+( entity )
+( environment )
+( environmental process )
+( epidemiology )
+( equipment )
+( ethnic group )
+( eukaryote )
+( event )
+( event history )
+( except advertising )
+( except aircraft and marine engines )
+( except aircraft and marine turbines )
+( except construction )
+( except electrical )
+( except lawyer or judge )
+( except motor vehicle )
+( except oil and gas wells )
+( except photo - gravers )
+( except rubber )
+( except ships ' engines )
+( except tire maker / tire vulcanizer )
+( except tire makers and tire vulcanisers )
+( except tire makers and tire vulcanizers )
+( except transport )
+( experimental )
+( experimental system )
+( exposure / injury )
+( extensiveness )
+( external anatomical feature )
+( eye )
+( family )
+( family issue )
+( female )
+( field )
+( fiinding )
+( film )
+( films )
+( finding )
+( findings )
+( fish )
+( flies )
+( flower )
+( follower of religion - person )
+( food )
+( for any age )
+( for cleaning purpose )
+( for gunter ' s chain )
+( for pain relief )
+( for staff )
+( for transmitting doses for pharmacokinetics )
+( formal meetings )
+( formation )
+( foundry )
+( freight train )
+( frequency )
+( fruit )
+( function )
+( function )
+( fungi hosts )
+( fungus )
+( garment )
+( gauge size )
+( general )
+( generic version )
+( genetics )
+( genu )
+( geographic )
+( geographic area )
+( geographic location )
+( glandula suprarenalis )
+( goal )
+( grade )
+( gramineae hosts )
+( grooming )
+( grooming )
+( group )
+( group of parts )
+( guideline )
+( gunter ' s chain )
+( hand - operated machine )
+( heading )
+( health )
+( health care )
+( healthcare )
+( helper cells )
+( hemorrhage )
+( high voltage )
+( histology )
+( history )
+( horizontal architectural support )
+( horse )
+( hosiery )
+( human only )
+( hypothalamus )
+( i . q . . . . . )
+( iadl finding )
+( idea )
+( identifier )
+( image )
+( in-store merchandise )
+( in animal tissues )
+( in vivo )
+( including digits )
+( indicator )
+( infection )
+( injury )
+( input )
+( inquiry )
+( insect )
+( insect hosts )
+( instep )
+( instruction )
+( instruction imperative )
+( intake )
+( interactions )
+( intercourse )
+( invertebrate )
+( island )
+( january 2007 release )
+( kind of quantity )
+( lab finding )
+( lab procedure )
+( lab result )
+( lab technique )
+( lab test )
+( laboratory finding )
+( laboratory procedure )
+( land - based )
+( laparotomy performed )
+( length )
+( lepidoptora hosts )
+( libraries )
+( libraries )
+( life event - finding )
+( life style )
+( line - film )
+( lingual , palatine , pharyngeal )
+( link assertion )
+( linkage concept )
+( liquid )
+( list bullets )
+( list separately in addition to code for primary procedure )
+( living organism )
+( location )
+( logging )
+( long - distance transport )
+( lower case a )
+( machine )
+( machine , except jacquard loom )
+( machines )
+( male )
+( malting )
+( mammal )
+( mapping )
+( marine pseudomonad hosts )
+( masonry and woodwork )
+( material )
+( mating )
+( measurement )
+( medical device )
+( medically )
+( medium of exchange )
+( medulla )
+( medullae )
+( medullary reticular formation )
+( member of religious order )
+( membrane )
+( mental function )
+( mental process )
+( metabolim test )
+( metal )
+( metal melting , except cupola )
+( metal reheating )
+( method )
+( military )
+( mine )
+( mine / quarry )
+( mine and quarry )
+( minor structure )
+( miscellaneous )
+( modified )
+( modifier )
+( molecular function )
+( molecular structure )
+( morphologic abnormality )
+( morphologic abnormality , calcified structure )
+( morphology )
+( motion )
+( motion picture )
+( motivation )
+( musical )
+( nanoparticle )
+( natural and artificial )
+( nature of procedure values )
+( navigational concept )
+( neck )
+( nmo )
+( non-ferrous metals )
+( non medication )
+( nonoperative )
+( not alarm reaction )
+( number )
+( numerical qualifier )
+( object )
+( observable )
+( observable entity )
+( observation )
+( observation or disorder )
+( occasion for eating )
+( occupation )
+( occupation history )
+( occupation or discipline )
+( occupational group )
+( ocular )
+( oil / gas wells )
+( oil and gas wells )
+( oilfield )
+( oils and fats )
+( old people ' s home )
+( operative )
+( or )
+( oral challenge )
+( ore smelting )
+( organ )
+( organ component )
+( organ part )
+( organisation )
+( organism )
+( organization )
+( origin )
+( origins )
+( orthodontic procedure )
+( other )
+( output )
+( package insert )
+( pairs )
+( pairs )
+( palatine )
+( parameter )
+( part organ )
+( patient )
+( patient instructions )
+( pdq )
+( per time )
+( per volume )
+( person )
+( personality )
+( persons )
+( pertaining to a node )
+( petroleum refining )
+( phenomenon )
+( philosophy )
+( physical activity )
+( physical activity )
+( physical device )
+( physical finding )
+( physical force )
+( physical force )
+( physical geography )
+( physical object )
+( physical object )
+( physician )
+( physician group )
+( physiologic )
+( physiologic function )
+( physiology )
+( planet )
+( plant )
+( plant hosts )
+( plant part )
+( plants hosts )
+( platelet )
+( polypectomy )
+( population )
+( population )
+( population group )
+( position )
+( postinfection )
+( postoperative )
+( potency unit )
+( power station )
+( ppc - c )
+( prescription )
+( present illness )
+( present time )
+( press / radio / t . v . )
+( primary )
+( primary procedure )
+( printing )
+( private service )
+( procedure )
+( procedure detail )
+( procedure or disorder )
+( process )
+( process of discrimination )
+( product )
+( profession )
+( property )
+( property of measurement )
+( prosthesis )
+( protons , ions )
+( protozoa )
+( provider role )
+( psychiatric )
+( psychiatry )
+( psychologic )
+( psychological function )
+( psychology )
+( psychophysiology )
+( psychotherapy )
+( publication )
+( publication format )
+( publications )
+( pure mathematics )
+( qualifier )
+( qualifier in lnc )
+( qualifier value )
+( qualifier value )
+( quality )
+( race )
+( racial group )
+( radio / t . v . )
+( radio / television )
+( radio / television / radar equipment )
+( radio broadcasts )
+( radioactive materials )
+( radiologist )
+( rate )
+( reassigned )
+( record )
+( record artifact )
+( recreational activity )
+( reference documentation )
+( regime / therapy )
+( region )
+( region of foot )
+( rehabilitation )
+( reimbursement )
+( relative )
+( religion )
+( religion / philosophy )
+( reptile )
+( respiratory measure )
+( response modality )
+( result )
+( revised )
+( rifle )
+( road )
+( role )
+( rolling mill )
+( route )
+( route of administration )
+( schedule frequency )
+( science )
+( scotland )
+( sea )
+( season )
+( second level )
+( section of report )
+( self - care status )
+( sensation )
+( separate procedure )
+( serotype )
+( serous membrane )
+( services standards )
+( set of actions )
+( severe )
+( severity modifier )
+( shape )
+( shin )
+( ship )
+( singles )
+( site )
+( site of care )
+( situation )
+( sleep disorder )
+( slowed )
+( small pieces )
+( snails )
+( social behavior )
+( social concept )
+( social status )
+( sound )
+( sound intensity )
+( source type )
+( spatial )
+( special concept )
+( specialised )
+( specialized )
+( specialty )
+( specific stage )
+( specify )
+( specify level )
+( specify type )
+( specimen )
+( specimen source code )
+( spice )
+( sport )
+( sports activity )
+( stage / studio )
+( stage and studio )
+( staging scale )
+( statement )
+( statistical )
+( statistical adjustment )
+( statistical procedure )
+( statistical technique )
+( status )
+( steam )
+( steel )
+( steel converting )
+( steel refining )
+( still camera )
+( strain )
+( structure )
+( subdivision )
+( substance )
+( substance / material )
+( substance status )
+( substantia innominata )
+( substitution condition )
+( suffix )
+( sugar refining )
+( suppressor cells )
+( surface )
+( surface region )
+( surface region of back )
+( surgical )
+( surgical procedure )
+( surgical speciality )
+( surgical view )
+( symbol )
+( symptom )
+( system )
+( taxon )
+( technician / technologist )
+( techniques )
+( temporal )
+( temporal concept )
+( temporal qualifier )
+( terminology entity )
+( test result )
+( testicles )
+( theater )
+( theatre )
+( theoretical )
+( therapeutic )
+( therapy )
+( therapy ) ( diagnostic id )
+( third level )
+( time frame )
+( time pattern )
+( time period )
+( time point or interval )
+( tissue )
+( tissue integrity )
+( to be done prior to surgery )
+( traffic )
+( transanal disk excision )
+( transmission )
+( transportation )
+( treatment )
+( trust territory )
+( tumor staging )
+( type )
+( type of material , substance )
+( u . s . )
+( uniformity )
+( unit )
+( unit of mass )
+( unit of measure )
+( unit of pressure )
+( unmodified )
+( upper )
+( us )
+( use calc )
+( use of drug )
+( use only with codes for immunization )
+( used to identify procedures performed on the left side of the body )
+( used to identify procedures performed on the right side of the body )
+( uterine )
+( value )
+( variant )
+( vegetable )
+( version 4 )
+( vertebral column )
+( vertebrale )
+( vocalization )
+( volume )
+( wait and see )
+( wasp )
+( waterworks )
+( weight )
+( wood distillation )
+( workshop )
+( yes / no )
+( zoology )
+,
+, cs
+, device
+, disorder
+, follower of religion
+, function
+, life event
+, services & procedure codes ( category iii , temporary )
+, united states
+[ any part ]
+[ a body part ]
+[ action ]
+[ activity ]
+[ adjective ]
+[ an instruction material ]
+[ any part ]
+[ artwork ]
+[ ball ]
+[ body ]
+[ body function ]
+[ body part ]
+[ body parts ]
+[ character ]
+[ chemical / ingredient ]
+[ clothing ]
+[ color ]
+[ device ]
+[ disease / finding ]
+[ document ]
+[ dose form ]
+[ economics ]
+[ environment ]
+[ executive duty ]
+[ extent ]
+[ finding ]
+[ fish ]
+[ follower of religion ]
+[ for organism ( & culture ) ]
+[ furniture ]
+[ game ]
+[ garment ]
+[ hiv ]
+[ in an environmental context ]
+[ in social context ]
+[ mammal ]
+[ manufactured object ]
+[ manufactured product ]
+[ mating posture ]
+[ medical device ]
+[ mental function ]
+[ mental process ]
+[ moa ]
+[ molecular function ]
+[ money ]
+[ motion ]
+[ ngu ]
+[ object ]
+[ occupation ]
+[ organism ] or [ infection - shingles ]
+[ organization ]
+[ paper report ]
+[ pe ]
+[ people ]
+[ physical phenomenon ]
+[ plan ]
+[ plant ]
+[ procedure ]
+[ product ]
+[ profession ]
+[ psychology ]
+[ publication type ]
+[ race ]
+[ reference materials ]
+[ room ]
+[ sample ]
+[ specialty ]
+[ sports ]
+[ statistical concept ]
+[ status ]
+[ substance ]
+[ surgical action ]
+[ uniformity ]
+[ unit of measurement ]
+[ unit of pressure ]
+] ( person )
+{ organization ]
+< subjective >
+epidemiology
+status ( & consent )
+// Added for Tim Other
+( research activity )
+( social )
+( cardiorsp )
+( glass microscope )
+( social event )
+( research methods )
+( microwave )
+( sexual orientation )
+( life event )
+[ va product ]
+( & to doctor )
+( & aids - daily life use )
+( & trauma )
+( & status )
+( & gastroscopy )
+( & thyroxine )
+( & repeat prescription )
+& ( fitting )
+( & loan )
+( & laboratory tests )
+& # 124 ; patient
+& # 124 ; { dental arch }
+& # 124 ; dentition
+& # 124 ; endocrine system
+& # 124 ; tube
+& # 124 ; ear , nose , throat
+& # 124 ; genitourinary
+& # 124 ; ?
+& # 124 ; cardiovascular system
+& # 124 ; cancer xxx
+& # 124 ; xxx
+& # 124 ; blood product unit
+& # 124 ; behavior
+& # 124 ; gingiva
+& # 124 ; stomach
+& # 124 ; nervous system
+& # 124 ; measurement
+& # 124 ; ear
+& # 124 ; { event }
+{ event }
+& # 124 ;
+, 3s
+( individual study )
+[ medical specialty ]
+( multiple patients )
+( by report )
+( no selection ; dispense as written )
+; per 15 minutes
+// , per 15 minutes
+; per 15 min
+// , per 15 min
+// , 15 min
+/ 15min
+; per diem
+// , per diem
+/ diem
+; per hour
+// , per hour
+// , per hr
+; each session
+; per service
+; per month
+- statement of investigator
+( & processing )
+( restaurants )
+( phonetics )
+( cataloging )
+( chemistry )
+( leisure )
+( vehicles )
+( occult sciences )
+( information services )
+( sodium chloride )
+( better )
+( e . g . fiber )
+( dose pack container )
+( waterproof layer in domestic structure )
+( flight )
+( psychosocial )
+( unconditioned )
+( prescribed )
+misc . each
+, nos , each
+nos each
+each
+/ psychosocial function observable
+misc . oil
+100g
+& # 124 ; bld - ser - plas
+( dietary substance )
+0 . 9 %
+( ml )
+- substance
+( poultry )
+[ food ]

Added: ctakes/sandbox/dictionary-gui/data/tim/emptyAnatTuis.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tim/emptyAnatTuis.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tim/emptyAnatTuis.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tim/emptyAnatTuis.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1 @@
+// No desired anatomy tuis
\ No newline at end of file

Added: ctakes/sandbox/dictionary-gui/data/tiny/ConversionSources.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tiny/ConversionSources.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tiny/ConversionSources.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tiny/ConversionSources.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,4 @@
+ICD10PCS
+ICD9CM
+RXNORM
+SNOMEDCT_US
\ No newline at end of file

Added: ctakes/sandbox/dictionary-gui/data/tiny/CtakesAnatTuis.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tiny/CtakesAnatTuis.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tiny/CtakesAnatTuis.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tiny/CtakesAnatTuis.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,8 @@
+T021
+T022
+T023
+T024
+T025
+T026
+T029
+T030

Added: ctakes/sandbox/dictionary-gui/data/tiny/CtakesDrugTuis.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tiny/CtakesDrugTuis.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tiny/CtakesDrugTuis.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tiny/CtakesDrugTuis.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,22 @@
+T109
+T110
+T114
+T115
+T116
+T118
+T119
+T121
+T122
+T123
+T124
+T125
+T126
+T127
+T129
+T130
+T131
+T195
+T196
+T197
+T200
+T203

Added: ctakes/sandbox/dictionary-gui/data/tiny/CtakesSnomedTuis.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tiny/CtakesSnomedTuis.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tiny/CtakesSnomedTuis.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tiny/CtakesSnomedTuis.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,36 @@
+// ANAT
+// T021
+// T022
+// T023
+// T024
+// T025
+// T026
+// T029
+// T030
+// DISO
+T019
+T020
+T037
+T047
+T048
+T049
+T050
+T190
+T191
+// FIND
+T033
+T034
+T040
+T041
+T042
+T043
+T044
+T045
+T046
+T056
+T057
+T184
+// PROC
+T059
+T060
+T061

Added: ctakes/sandbox/dictionary-gui/data/tiny/CtakesSources.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tiny/CtakesSources.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tiny/CtakesSources.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tiny/CtakesSources.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,4 @@
+SNOMEDCT
+SNOMEDCT_US
+ICD9CM
+ICD10PCS

Added: ctakes/sandbox/dictionary-gui/data/tiny/ModifierSuffixes.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tiny/ModifierSuffixes.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tiny/ModifierSuffixes.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tiny/ModifierSuffixes.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1 @@
+// Don't automatically modify for tiny

Added: ctakes/sandbox/dictionary-gui/data/tiny/RemovalColonTriggers.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tiny/RemovalColonTriggers.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tiny/RemovalColonTriggers.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tiny/RemovalColonTriggers.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,38 @@
+: - :
+: 24 hours :
+: 8 hours :
+: address :
+: arbitrary concentration :
+: duration of encounter :
+: duration of the study :
+: finding :
+: identifier :
+: impression / interpretation of study :
+: life of the unit :
+: mass :
+: number :
+: point in time :
+: prid :
+: pt :
+: substance concentration :
+: text :
+: type :
+: volume :
+: volume rate :
+// The following are in UnwantedSuffixes for default, but trigger removal for tiny
+:
+: - -
+: - : point in time : ^ patient : - : phenx
+: ( & glucose ( & plasma ) )
+: ( & nos )
+: [ & named variants ]
+: [ admin ] or [ exam ]
+: [ drivers exam ] or [ dtp20003 - hgv / publ serv claim ] or [ admin ]
+: [ early morning ] or [ mid-stream ] or [ for organism ( & culture ) ]
+: [ exam ( & admin ) ] ) or [ my22 form ]
+: [ fp78 ] or [ gp78 ]
+: [ implantation ] or [ implant ]
+: [ monitoring ] or [ clinic ]
+: [ nos ]
+: [ officer ] or [ executive ]
+: [ production ] or [ product ]

Added: ctakes/sandbox/dictionary-gui/data/tiny/RemovalFunctionTriggers.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tiny/RemovalFunctionTriggers.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tiny/RemovalFunctionTriggers.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tiny/RemovalFunctionTriggers.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,4 @@
+] or [
+] & / or [
+) or (
+) & / or (
\ No newline at end of file

Added: ctakes/sandbox/dictionary-gui/data/tiny/RemovalPrefixTriggers.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tiny/RemovalPrefixTriggers.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tiny/RemovalPrefixTriggers.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tiny/RemovalPrefixTriggers.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,37 @@
+deprecated 
+retired procedure
+// The following are in UnwantedPrefixes for the default, but removed for small
+[ d ]
+[ edta ]
+[ m ]
+[ q ]
+[ v ]
+[ x ]
+[ so ]
+activities involving
+and unspecified
+( non-specific )
+child :
+college of american pathologists cancer checklist ;
+other activity involving
+other
+phenx -
+specimen source code -
+specimen source codes -
+specimen source codes =
+ or
+#
+&
+& [
+'
+*
+-
+:
+?
+// The following are in UnwantedPrefixes for the default, but removed for tiny
+// The idea is that such prefixes would most likely not be found by the old dictionary
+// And there should be versions without these prefixes
+( congenital )
+engaged in
+entire
+h / o :

Added: ctakes/sandbox/dictionary-gui/data/tiny/RemovalSuffixTriggers.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tiny/RemovalSuffixTriggers.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tiny/RemovalSuffixTriggers.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tiny/RemovalSuffixTriggers.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,1017 @@
+- retired code
+- retired -
+- retired
+( reassigned )
+[ obsolete ]
+( deprecated )
+// The following are in UnwantedSuffixes for default, but trigger removal for small
+- ( other )
+- duplicate -
+- nos
+- retired
+- retired -
+- unspec
+- unspecified
+ as topic
+ as topics
+ nec
+ nec in snomedct
+ nos
+ not otherwise specified
+ or
+ title 18
+( or )
+( 10 )
+( _ _ _ 0 , 2 )
+( deprecated )
+( except leather and fur )
+( hl7v3 . 0 concept )
+( inactive concept )
+( mesh category )
+( namespace concept )
+( non-specific )
+( nos )
+( not elsewhere classified in lnc )
+( obsolete notation )
+( procedure nec )
+( process of differentiation )
+) ( adjudicators ( & top )
+& / or o / e
+& / or orderly ( & [ orderlies ] )
+& [ fistula ]
+& [ symptom ]
+& [ legal ]
+& [ symptom ]
+& [ vehicle ]
+( & [ reimbursement ] )
+( & [ abnormal ] )
+( & [ acquired ] )
+( & [ acute ] )
+( & [ acute nos ] )
+( & [ broad ligament ] )
+( & [ bupa examination done ] )
+( & [ c / o - ] )
+( & [ c / o ] )
+( & [ chart ] )
+( & [ duct ] or [ gland ] )
+( & [ eating observation ] )
+( & [ etc ] )
+( & [ expiratory ] )
+( & [ eye disorder ] )
+( & [ government ] )
+( & [ hall ] )
+( & [ infection ] )
+( & [ keen ] )
+( & [ labor complicated by ] )
+( & [ laborer nos ] )
+( & [ labour complicated by ] )
+( & [ labourer nos ] )
+( & [ machine ] and / or [ press ] )
+( & [ member of phct ] )
+( & [ miners ( & coal )
+( & [ named variants ] )
+( & [ nec ] )
+( & [ nos ] )
+( & [ obstructive ] )
+( & [ occupation ] )
+( & [ occupations ] )
+( & [ officer ] )
+( & [ product ] )
+( & [ refer ] )
+( & [ referral ] )
+( & [ referral to ] )
+( & [ reimbursement ] )
+( & [ retail ] )
+( & [ rubber ] )
+( & [ staff ] )
+( & [ staghorn ] )
+( & [ symptom ] )
+( & [ teachers ] )
+( & [ unmarried ] )
+( & [ unspecified ] )
+( & [ warfarin ] )
+( & [ weightlessness ] )
+( & [ well ] )
+( & acquired )
+( & acute )
+( & admin )
+( & administration )
+( & ankle joint )
+( & assess )
+( & attic )
+( & bladder )
+( & blind )
+( & c / o )
+( & c / s )
+( & certificate )
+( & chronic )
+( & claim )
+( & claim gp / ms )
+( & congenital )
+( & conjunctiva )
+( & consent )
+( & dialysis )
+( & direct )
+( & disorder )
+( & distal )
+( & drug )
+( & expiratory )
+( & f303 )
+( & floor / wall )
+( & food poison )
+( & form )
+( & form gp45 ) )
+( & form : [ fp70a ] or [ gp / pea ] )
+( & from patient )
+( & held )
+( & hepatic duct )
+( & in blood )
+( & infection )
+( & infestation )
+( & level ( & phenylalanine ) )
+( & level )
+( & localization )
+( & marital )
+( & maternity allowances )
+( & mobile unit x-ray )
+( & named variants )
+( & nec )
+( & non urg )
+( & nos )
+( & o / e )
+( & on medical advice )
+( & operation )
+( & other )
+( & pathology )
+( & patient data )
+( & peritonsillar region )
+( & pleural )
+( & provision )
+( & record )
+( & referred to )
+( & report )
+( & result )
+( & sample )
+( & sc1 - given to staff )
+( & scrotal skin )
+( & short hip rotator )
+( & sinus )
+( & skin )
+( & skin of external ear )
+( & skin of external nose )
+( & skin of eyebrow )
+( & skin of eyelid )
+( & skin of male perineum )
+( & skin of nipple )
+( & skin of penis )
+( & skin of vulva )
+( & stock order gp10a )
+( & swab )
+( & symptom )
+( & tanner )
+( & top )
+( & top managers )
+( & traumatic )
+( & umbilical skin )
+( & unspecified )
+( & upper )
+( & vaccination )
+( & various types )
+( & viral )
+( & with stabilisation )
+( & with stabilization )
+( * )
+( _ _ _ per hpf )
+( + / - religion )
+( = breath )
+( = breath )
+( = stone )
+( = stone )
+[ & aircraft ]
+[ & bacterial ]
+[ & glucose ]
+[ & named variants ]
+[ & nos ]
+[ & professional ]
+[ & symptom ]
+[ ambiguous ]
+[ dup ]
+[ duplicate ]
+[ obsolete ]
+[ other ]
+, nec in snomedct
+, nos
+, not elsewhere classified
+, unclassified
+, unspecified
+, unspecified part
+concept ( inactive concept )
+reason not stated ( inactive concept )
+// New for small
+&
+// The following are in UnwantedSuffixes for the default, but removed for tiny
+// The idea is that such suffixes would most likely not be found by the old dictionary
+// And there should be versions without these suffixes
+- ( religious affiliation )
+- a specialty area of medicine
+- action
+- activity of daily living
+- assess ( & non urg )
+- attribute
+- biologic function
+- category
+- confectionery
+- dietary
+- entertainment ( & [ musical ]
+- finding
+- function
+- general -
+- herbal supplement
+- mental defense mechanism
+- mental process
+- observation
+- organization
+- physical agent
+- related finding
+- rolecode
+- speciality
+- specialty
+- summary
+- symptom
+- weather
+- sport
+( a priority lower than stat )
+( abnormality )
+( abo blood group )
+( acholeplasma host )
+( acknowledgementcondition )
+( acquired )
+( action )
+( action )
+( activated )
+( activity )
+( activity )
+( actual )
+( adjudicators ( & top )
+( adl finding )
+( administative )
+( administration method )
+( administrative concept )
+( age group )
+( alcohol )
+( all components )
+( all fractions of )
+( allelic variant )
+( alone )
+( alphabetic group )
+( alternative )
+( amount )
+( amphibian )
+( anatomical classification )
+( anatomical coordinate )
+( anatomical descriptor )
+( anatomical feature )
+( anatomical location )
+( anatomy )
+( and accessories )
+( and related agents )
+( angiosperm hosts )
+( animal )
+( any part )
+( apparatus )
+( applies to non-numeric results )
+( area of increased mortality )
+( area of knowledge )
+( arrangement )
+( art )
+( artificial )
+( artistic )
+( ascomycota )
+( assessment )
+( assessment scale )
+( astronomy )
+( at present )
+( attitude )
+( attribute )
+( attributes )
+( audit )
+( australia )
+( available ( qualifier ) )
+( bacteria )
+( bacteria and cyanobacteria hosts )
+( battery - powered )
+( beach )
+( beach , court )
+( beet sugar )
+( behavior )
+( behavior finding )
+( beverage )
+( biologic function )
+( biological )
+( biological function )
+( biological funtion )
+( biopsy result )
+( bird )
+( blacus )
+( blood components )
+( blood pressure )
+( body part )
+( body structure )
+( body substance )
+( botanical taxonomic category below variety )
+( brain )
+( brain structure )
+( button )
+( calcified structure )
+( canal )
+( cancer stage )
+( candy )
+( cardiac conduction )
+( category )
+( catering and lodging services )
+( cell )
+( cell line )
+( cell structure )
+( cells or organisms )
+( central nervous system tumor )
+( central nervous system tumour )
+( cerebellum )
+( certification )
+( change )
+( characteristic )
+( chemical )
+( chemical / related processes )
+( chemical and related processes )
+( chemical processes , except petroleum )
+( citrus )
+( class )
+( classical )
+( classification )
+( cleansing action )
+( clinical )
+( clinical definition )
+( clinical disorder )
+( clinical specialty )
+( color )
+( combined site )
+( comfort level finding )
+( communication )
+( communicationfunctiontype )
+( community )
+( company )
+( compartment )
+( complement activation )
+( complete ) ( partial )
+( component )
+( composite )
+( compression algorithm )
+( computer )
+( computer files directory )
+( computer network )
+( concept )
+( construction )
+( container status )
+( containing tobacco )
+( context - dependent category )
+( contextual qualifier )
+( copy in notes )
+( copy within chart )
+( court )
+( crustacea )
+( crustacean )
+( data - processing )
+( data )
+( data type )
+( dataset )
+( dedicated instruments )
+( degree / certification )
+( degree / license / certification )
+( dental procedure )
+( detection and tagging )
+( deviation )
+( device )
+( device status )
+( diagnosis )
+( diagnostic , surgical , and therapeutic interventions )
+( dicotyledons hosts )
+( dietary )
+( digestive structure of animal )
+( diminutive )
+( direction )
+( discharge )
+( discipline )
+( disease )
+( disease attribute )
+( diskus intervertebralis )
+( disorder )
+( do as near as possible to requested time )
+( do immediately )
+( document )
+( document type )
+( documents )
+( dry - cleaner )
+( dysfunction )
+( economic )
+( economic descriptor )
+( economic status )
+( edible )
+( edible oils )
+( education )
+( electric power )
+( electrical )
+( embryology )
+( embryonic structure )
+( emergency )
+( emotion )
+( emotional response )
+( end postition )
+( england & wales )
+( england and wales )
+( entertainment )
+( entire collection )
+( entity )
+( environment )
+( environmental process )
+( epidemiology )
+( equipment )
+( ethnic group )
+( eukaryote )
+( event )
+( event history )
+( except advertising )
+( except aircraft and marine engines )
+( except aircraft and marine turbines )
+( except construction )
+( except electrical )
+( except lawyer or judge )
+( except motor vehicle )
+( except oil and gas wells )
+( except photo - gravers )
+( except rubber )
+( except ships ' engines )
+( except tire maker / tire vulcanizer )
+( except tire makers and tire vulcanisers )
+( except tire makers and tire vulcanizers )
+( except transport )
+( experimental )
+( experimental system )
+( exposure / injury )
+( extensiveness )
+( external anatomical feature )
+( eye )
+( family )
+( family issue )
+( female )
+( field )
+( fiinding )
+( film )
+( films )
+( finding )
+( findings )
+( fish )
+( flies )
+( flower )
+( follower of religion - person )
+( food )
+( for any age )
+( for cleaning purpose )
+( for gunter ' s chain )
+( for pain relief )
+( for staff )
+( for transmitting doses for pharmacokinetics )
+( formal meetings )
+( formation )
+( foundry )
+( freight train )
+( frequency )
+( fruit )
+( function )
+( function )
+( fungi hosts )
+( fungus )
+( garment )
+( gauge size )
+( general )
+( generic version )
+( genetics )
+( genu )
+( geographic )
+( geographic area )
+( geographic location )
+( glandula suprarenalis )
+( goal )
+( grade )
+( gramineae hosts )
+( grooming )
+( grooming )
+( group )
+( group of parts )
+( guideline )
+( gunter ' s chain )
+( hand - operated machine )
+( heading )
+( health )
+( health care )
+( healthcare )
+( helper cells )
+( hemorrhage )
+( high voltage )
+( histology )
+( history )
+( horizontal architectural support )
+( horse )
+( hosiery )
+( human only )
+( hypothalamus )
+( i . q . . . . . )
+( iadl finding )
+( idea )
+( identifier )
+( image )
+( in-store merchandise )
+( in animal tissues )
+( in vivo )
+( including digits )
+( indicator )
+( infection )
+( injury )
+( input )
+( inquiry )
+( insect )
+( insect hosts )
+( instep )
+( instruction )
+( instruction imperative )
+( intake )
+( interactions )
+( intercourse )
+( invertebrate )
+( island )
+( january 2007 release )
+( kind of quantity )
+( lab finding )
+( lab procedure )
+( lab result )
+( lab technique )
+( lab test )
+( laboratory finding )
+( laboratory procedure )
+( land - based )
+( laparotomy performed )
+( length )
+( lepidoptora hosts )
+( libraries )
+( libraries )
+( life event - finding )
+( life style )
+( line - film )
+( lingual , palatine , pharyngeal )
+( link assertion )
+( linkage concept )
+( liquid )
+( list bullets )
+( list separately in addition to code for primary procedure )
+( living organism )
+( location )
+( logging )
+( long - distance transport )
+( lower case a )
+( machine )
+( machine , except jacquard loom )
+( machines )
+( male )
+( malting )
+( mammal )
+( mapping )
+( marine pseudomonad hosts )
+( masonry and woodwork )
+( material )
+( mating )
+( measurement )
+( medical device )
+( medically )
+( medium of exchange )
+( medulla )
+( medullae )
+( medullary reticular formation )
+( member of religious order )
+( membrane )
+( mental function )
+( mental process )
+( metabolim test )
+( metal )
+( metal melting , except cupola )
+( metal reheating )
+( method )
+( military )
+( mine )
+( mine / quarry )
+( mine and quarry )
+( minor structure )
+( miscellaneous )
+( modified )
+( modifier )
+( molecular function )
+( molecular structure )
+( morphologic abnormality )
+( morphologic abnormality , calcified structure )
+( morphology )
+( motion )
+( motion picture )
+( motivation )
+( musical )
+( nanoparticle )
+( natural and artificial )
+( nature of procedure values )
+( navigational concept )
+( neck )
+( nmo )
+( non-ferrous metals )
+( non medication )
+( nonoperative )
+( not alarm reaction )
+( number )
+( numerical qualifier )
+( object )
+( observable )
+( observable entity )
+( observation )
+( observation or disorder )
+( occasion for eating )
+( occupation )
+( occupation history )
+( occupation or discipline )
+( occupational group )
+( ocular )
+( oil / gas wells )
+( oil and gas wells )
+( oilfield )
+( oils and fats )
+( old people ' s home )
+( operative )
+( or )
+( oral challenge )
+( ore smelting )
+( organ )
+( organ component )
+( organ part )
+( organisation )
+( organism )
+( organization )
+( origin )
+( origins )
+( orthodontic procedure )
+( other )
+( output )
+( package insert )
+( pairs )
+( pairs )
+( palatine )
+( parameter )
+( part organ )
+( patient )
+( patient instructions )
+( pdq )
+( per time )
+( per volume )
+( person )
+( personality )
+( persons )
+( pertaining to a node )
+( petroleum refining )
+( phenomenon )
+( philosophy )
+( physical activity )
+( physical activity )
+( physical device )
+( physical finding )
+( physical force )
+( physical force )
+( physical geography )
+( physical object )
+( physical object )
+( physician )
+( physician group )
+( physiologic )
+( physiologic function )
+( physiology )
+( planet )
+( plant )
+( plant hosts )
+( plant part )
+( plants hosts )
+( platelet )
+( polypectomy )
+( population )
+( population )
+( population group )
+( position )
+( postinfection )
+( postoperative )
+( potency unit )
+( power station )
+( ppc - c )
+( prescription )
+( present illness )
+( present time )
+( press / radio / t . v . )
+( primary )
+( primary procedure )
+( printing )
+( private service )
+( procedure )
+( procedure detail )
+( procedure or disorder )
+( process )
+( process of discrimination )
+( product )
+( profession )
+( property )
+( property of measurement )
+( prosthesis )
+( protons , ions )
+( protozoa )
+( provider role )
+( psychiatric )
+( psychiatry )
+( psychologic )
+( psychological function )
+( psychology )
+( psychophysiology )
+( psychotherapy )
+( publication )
+( publication format )
+( publications )
+( pure mathematics )
+( qualifier )
+( qualifier in lnc )
+( qualifier value )
+( qualifier value )
+( quality )
+( race )
+( racial group )
+( radio / t . v . )
+( radio / television )
+( radio / television / radar equipment )
+( radio broadcasts )
+( radioactive materials )
+( radiologist )
+( rate )
+( reassigned )
+( record )
+( record artifact )
+( recreational activity )
+( reference documentation )
+( regime / therapy )
+( region )
+( region of foot )
+( rehabilitation )
+( reimbursement )
+( relative )
+( religion )
+( religion / philosophy )
+( reptile )
+( respiratory measure )
+( response modality )
+( result )
+( revised )
+( rifle )
+( road )
+( role )
+( rolling mill )
+( route )
+( route of administration )
+( schedule frequency )
+( science )
+( scotland )
+( sea )
+( season )
+( second level )
+( section of report )
+( self - care status )
+( sensation )
+( separate procedure )
+( serotype )
+( serous membrane )
+( services standards )
+( set of actions )
+( severe )
+( severity modifier )
+( shape )
+( shin )
+( ship )
+( singles )
+( site )
+( site of care )
+( situation )
+( sleep disorder )
+( slowed )
+( small pieces )
+( snails )
+( social behavior )
+( social concept )
+( social status )
+( sound )
+( sound intensity )
+( source type )
+( spatial )
+( special concept )
+( specialised )
+( specialized )
+( specialty )
+( specific stage )
+( specify )
+( specify level )
+( specify type )
+( specimen )
+( specimen source code )
+( spice )
+( sport )
+( sports activity )
+( stage / studio )
+( stage and studio )
+( staging scale )
+( statement )
+( statistical )
+( statistical adjustment )
+( statistical procedure )
+( statistical technique )
+( status )
+( steam )
+( steel )
+( steel converting )
+( steel refining )
+( still camera )
+( strain )
+( structure )
+( subdivision )
+( substance )
+( substance / material )
+( substance status )
+( substantia innominata )
+( substitution condition )
+( suffix )
+( sugar refining )
+( suppressor cells )
+( surface )
+( surface region )
+( surface region of back )
+( surgical )
+( surgical procedure )
+( surgical speciality )
+( surgical view )
+( symbol )
+( symptom )
+( system )
+( taxon )
+( technician / technologist )
+( techniques )
+( temporal )
+( temporal concept )
+( temporal qualifier )
+( terminology entity )
+( test result )
+( testicles )
+( theater )
+( theatre )
+( theoretical )
+( therapeutic )
+( therapy )
+( therapy ) ( diagnostic id )
+( third level )
+( time frame )
+( time pattern )
+( time period )
+( time point or interval )
+( tissue )
+( tissue integrity )
+( to be done prior to surgery )
+( traffic )
+( transanal disk excision )
+( transmission )
+( transportation )
+( treatment )
+( trust territory )
+( tumor staging )
+( type )
+( type of material , substance )
+( u . s . )
+( uniformity )
+( unit )
+( unit of mass )
+( unit of measure )
+( unit of pressure )
+( unmodified )
+( upper )
+( us )
+( use calc )
+( use of drug )
+( use only with codes for immunization )
+( used to identify procedures performed on the left side of the body )
+( used to identify procedures performed on the right side of the body )
+( uterine )
+( value )
+( variant )
+( vegetable )
+( version 4 )
+( vertebral column )
+( vertebrale )
+( vocalization )
+( volume )
+( wait and see )
+( wasp )
+( waterworks )
+( weight )
+( wood distillation )
+( workshop )
+( yes / no )
+( zoology )
+, cs
+, device
+, disorder
+, follower of religion
+, function
+, life event
+, services & procedure codes ( category iii , temporary )
+, united states
+[ any part ]
+[ a body part ]
+[ action ]
+[ activity ]
+[ adjective ]
+[ an instruction material ]
+[ any part ]
+[ artwork ]
+[ ball ]
+[ body ]
+[ body function ]
+[ body part ]
+[ body parts ]
+[ character ]
+[ chemical / ingredient ]
+[ clothing ]
+[ color ]
+[ device ]
+[ disease / finding ]
+[ document ]
+[ dose form ]
+[ economics ]
+[ environment ]
+[ executive duty ]
+[ extent ]
+[ finding ]
+[ fish ]
+[ follower of religion ]
+[ for organism ( & culture ) ]
+[ furniture ]
+[ game ]
+[ garment ]
+[ hiv ]
+[ in an environmental context ]
+[ in social context ]
+[ mammal ]
+[ manufactured object ]
+[ manufactured product ]
+[ mating posture ]
+[ medical device ]
+[ mental function ]
+[ mental process ]
+[ moa ]
+[ molecular function ]
+[ money ]
+[ motion ]
+[ ngu ]
+[ object ]
+[ occupation ]
+[ organism ] or [ infection - shingles ]
+[ organization ]
+[ paper report ]
+[ pe ]
+[ people ]
+[ physical phenomenon ]
+[ plan ]
+[ plant ]
+[ procedure ]
+[ product ]
+[ profession ]
+[ psychology ]
+[ publication type ]
+[ race ]
+[ reference materials ]
+[ room ]
+[ sample ]
+[ specialty ]
+[ sports ]
+[ statistical concept ]
+[ status ]
+[ substance ]
+[ surgical action ]
+[ uniformity ]
+[ unit of measurement ]
+[ unit of pressure ]
+] ( person )
+{ organization ]
+< subjective >
+epidemiology
+status ( & consent )
+

Added: ctakes/sandbox/dictionary-gui/data/tiny/RightAbbreviations.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tiny/RightAbbreviations.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tiny/RightAbbreviations.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tiny/RightAbbreviations.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1 @@
+// No automatic abbreviation extraction for tiny
\ No newline at end of file

Added: ctakes/sandbox/dictionary-gui/data/tiny/UnwantedPrefixes.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tiny/UnwantedPrefixes.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tiny/UnwantedPrefixes.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tiny/UnwantedPrefixes.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1 @@
+// No unwanted prefixes for tiny, only removal
\ No newline at end of file

Added: ctakes/sandbox/dictionary-gui/data/tiny/UnwantedSuffixes.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/data/tiny/UnwantedSuffixes.txt?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/data/tiny/UnwantedSuffixes.txt (added)
+++ ctakes/sandbox/dictionary-gui/data/tiny/UnwantedSuffixes.txt Sun Dec 13 04:27:42 2015
@@ -0,0 +1,4 @@
+/
+'
+-
+,

Added: ctakes/sandbox/dictionary-gui/lib/junit-4.12.jar
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/lib/junit-4.12.jar?rev=1719760&view=auto
==============================================================================
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Added: ctakes/sandbox/dictionary-gui/lib/log4j-api-2.5.jar
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/lib/log4j-api-2.5.jar?rev=1719760&view=auto
==============================================================================
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Added: ctakes/sandbox/dictionary-gui/lib/log4j-core-2.5.jar
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/lib/log4j-core-2.5.jar?rev=1719760&view=auto
==============================================================================
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Added: ctakes/sandbox/dictionary-gui/src/main/java/org/apache/ctakes/dictionary/creator/gui/ctakes/DictionaryBuilder.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/dictionary-gui/src/main/java/org/apache/ctakes/dictionary/creator/gui/ctakes/DictionaryBuilder.java?rev=1719760&view=auto
==============================================================================
--- ctakes/sandbox/dictionary-gui/src/main/java/org/apache/ctakes/dictionary/creator/gui/ctakes/DictionaryBuilder.java (added)
+++ ctakes/sandbox/dictionary-gui/src/main/java/org/apache/ctakes/dictionary/creator/gui/ctakes/DictionaryBuilder.java Sun Dec 13 04:27:42 2015
@@ -0,0 +1,156 @@
+package org.apache.ctakes.dictionary.creator.gui.ctakes;
+
+
+import org.apache.ctakes.dictionary.creator.gui.umls.*;
+import org.apache.ctakes.dictionary.creator.util.HsqlUtil;
+import org.apache.ctakes.dictionary.creator.util.RareWordDbWriter;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+/**
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 12/11/2015
+ */
+final public class DictionaryBuilder {
+
+   static private final Logger LOGGER = LogManager.getLogger( "DictionaryBuilder" );
+
+   static private final String DEFAULT_DATA_DIR = "./data/default";
+   static private final String CTAKES_APP_DB_PATH = "resources/org/apache/ctakes/dictionary/lookup/fast";
+   static private final String CTAKES_RES_MODULE = "ctakes-dictionary-lookup-fast-res";
+   static private final String CTAKES_RES_DB_PATH = CTAKES_RES_MODULE+"/src/main/" + CTAKES_APP_DB_PATH;
+   static private final int MIN_TERM_LENGTH = 2;
+   static private final int MIN_DRUG_TERM_LENGTH = 1;
+
+
+   private DictionaryBuilder() {}
+
+
+   static public boolean buildDictionary( final String umlsDirPath,
+                                          final String ctakesDirPath,
+                                          final String dictionaryName,
+                                          final Collection<String> wantedSources,
+                                          final Collection<String> wantedTargets,
+                                          final Collection<Tui> wantedTuis ) {
+      // Set up the term utility
+      final UmlsTermUtil umlsTermUtil = new UmlsTermUtil( DEFAULT_DATA_DIR );
+      final Map<Long,Concept> anatomies = parseAnatomy( umlsTermUtil, umlsDirPath, wantedSources, wantedTargets, wantedTuis );
+      final Map<Long,Concept> nonSpecials = parseNonSpecial( umlsTermUtil, umlsDirPath, wantedSources, wantedTargets, wantedTuis, anatomies
+            .values() );
+      final Map<Long,Concept> medications = parseMedication( umlsTermUtil, umlsDirPath, wantedTargets, wantedTuis );
+      writeDatabase( ctakesDirPath, dictionaryName, anatomies, nonSpecials, medications );
+
+//      Process process = ProcessBuilder( "java -Xmx2G -cp lib/hsqldb_1_8_0_10.jar org.hsqldb.util.SqlTool --rcfile " )
+      return true;
+   }
+
+   static private Map<Long,Concept> parseAnatomy( final UmlsTermUtil umlsTermUtil,
+                                                final String umlsDirPath,
+                                                final Collection<String> wantedSources,
+                                                final Collection<String> wantedTargets,
+                                                final Collection<Tui> wantedTuis ) {
+      LOGGER.info( "Parsing Anatomical Site Concepts" );
+      final Collection<Tui> wantedAnatTuis = new ArrayList<>( wantedTuis );
+      wantedAnatTuis.retainAll( Arrays.asList( TuiTableModel.CTAKES_ANAT ) );
+      final Map<Long,Concept> concepts = ConceptMapFactory.createConceptMap( umlsDirPath, wantedSources,
+            wantedAnatTuis, "Anatomical Site" );
+      // Fill in information for all valid concepts
+      MrconsoParser.parseConcepts( umlsDirPath, concepts, wantedTargets, umlsTermUtil, MIN_TERM_LENGTH, 7 );
+      LOGGER.info( "Done Parsing Anatomical Site Concepts" );
+      return concepts;
+   }
+
+   static private Map<Long,Concept> parseNonSpecial( final UmlsTermUtil umlsTermUtil,
+                                       final String umlsDirPath,
+                                       final Collection<String> wantedSources,
+                                        final Collection<String> wantedTargets,
+                                        final Collection<Tui> wantedTuis,
+                                        final Collection<Concept> anatomyConcepts ) {
+      LOGGER.info( "Parsing Non-Anatomical Site, Non-Medication Concepts" );
+      final Collection<Tui> wantedNormTuis = new ArrayList<>( wantedTuis );
+      wantedNormTuis.removeAll( Arrays.asList( TuiTableModel.CTAKES_ANAT ) );
+//      wantedNormTuis.removeAll( Arrays.asList( TuiTableModel.CTAKES_DRUG ) );
+      final Map<Long,Concept> concepts = ConceptMapFactory.createConceptMap( umlsDirPath, wantedSources,
+            wantedNormTuis, "Non-Anatomical Site, Non-Medication" );
+      // We don't want anatomical site texts to be anything but, so make them unavailable for other concepts
+      final Collection<String> anatomyTexts = anatomyConcepts.stream()
+            .map( Concept::getTexts )
+            .flatMap( Collection::stream )
+            .collect( Collectors.toSet() );
+      // Fill in information for all valid concepts
+      MrconsoParser.parseConcepts( umlsDirPath, concepts, wantedTargets, umlsTermUtil,
+            anatomyTexts, true, MIN_TERM_LENGTH, 7 );
+      LOGGER.info( "Done Parsing Non-Anatomical Site, Non-Medication Concepts" );
+      return concepts;
+   }
+
+   static private Map<Long,Concept> parseMedication( final UmlsTermUtil umlsTermUtil,
+                                        final String umlsDirPath,
+                                        final Collection<String> wantedTargets,
+                                        final Collection<Tui> wantedTuis ) {
+      LOGGER.info( "Parsing Medication Concepts" );
+      final Collection<Tui> wantedDrugTuis = new ArrayList<>( wantedTuis );
+      wantedDrugTuis.retainAll( Arrays.asList( TuiTableModel.CTAKES_DRUG ) );
+      final Map<Long,Concept> concepts = ConceptMapFactory.createRxConceptMap( umlsDirPath, wantedDrugTuis );
+      // Fill in information for all valid concepts
+      MrconsoParser.parseConcepts( umlsDirPath, concepts, wantedTargets, umlsTermUtil, MIN_DRUG_TERM_LENGTH, 11 );
+      // special case for nitric oxide "no"
+      final Concept nitricOxide = concepts.get( 28128l );
+      if ( nitricOxide != null ) {
+         nitricOxide.removeText( "no" );
+      }
+      LOGGER.info( "Done Parsing Medication Concepts" );
+      return concepts;
+   }
+
+   static private boolean writeDatabase( final String ctakesDirPath,
+                                         final String dictionaryName,
+                                         final Map<Long,Concept> anatomies,
+                                         final Map<Long,Concept> nonSpecials,
+                                         final Map<Long,Concept> medications ) {
+      mergeConcepts( nonSpecials, anatomies );
+      mergeConcepts( nonSpecials, medications );
+      return writeDatabase( ctakesDirPath, dictionaryName, nonSpecials );
+   }
+
+   static private boolean writeDatabase( final String ctakesDirPath,
+                                         final String dictionaryName,
+                                         final Map<Long,Concept> concepts ) {
+      final File ctakesRoot = new File( ctakesDirPath );
+      String databaseDirPath = ctakesDirPath + "/" + CTAKES_APP_DB_PATH;
+      if ( Arrays.asList( ctakesRoot.list() ).contains( CTAKES_RES_MODULE ) ) {
+         databaseDirPath = ctakesDirPath + "/" + CTAKES_RES_DB_PATH;
+      }
+      if ( !HsqlUtil.createDatabase( databaseDirPath, dictionaryName ) ) {
+         return false;
+      }
+      if ( !DictionaryXmlWriter.writeXmlFile( databaseDirPath, dictionaryName ) ) {
+         return false;
+      }
+      final String url = HsqlUtil.URL_PREFIX + databaseDirPath.replace( '\\', '/' ) + "/" + dictionaryName + "/" + dictionaryName;
+      return RareWordDbWriter.writeConcepts( concepts, url, "sa", "" );
+   }
+
+   static private void mergeConcepts( final Map<Long,Concept> mainConepts,
+                                      final Map<Long,Concept> mergingConcepts ) {
+      for ( Map.Entry<Long,Concept> mergable : mergingConcepts.entrySet() ) {
+         final Concept mainConcept = mainConepts.get( mergable.getKey() );
+         if ( mainConcept == null ) {
+            mainConepts.put( mergable.getKey(), mergable.getValue() );
+            continue;
+         }
+         mainConcept.mergeWith( mergable.getValue() );
+      }
+      mergingConcepts.clear();
+   }
+
+
+}



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