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From Nick Nikandish <snika...@emerginghealthit.com>
Subject RE: Retrieving CUIs
Date Tue, 08 Jul 2014 20:49:45 GMT
Thanks Pei,

I will change LookupDesc_Db.xml and test it right now.

-----Original Message-----
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu] 
Sent: Tuesday, July 08, 2014 4:45 PM
To: dev@ctakes.apache.org
Subject: RE: Retrieving CUIs

Nick,
On why 'Enterococcus faecium' isn't returned:
I think a limitation is that cTAKES will force a mapping of the TUI's semantic types into
a semantic group.  If it doesn't exist in the mapping, the dictionary lookup won't save it.
It would probably be a nice feature to create a "Other" semantic group and default anything
that is not mapped into this group.
You can test out this theory by modifying your LookupDesc_Db.xml to include T007 (Bacterium)
into one of the existing groups such findings and see if 'Enterococcus faecium' returns for
you.

[Assuming you're using the current default dictionary-lookup and not dictionary-lookup-fast]

> -----Original Message-----
> From: Nick Nikandish [mailto:snikandi@emerginghealthit.com]
> Sent: Tuesday, July 08, 2014 4:12 PM
> To: dev@ctakes.apache.org
> Subject: RE: Retrieving CUIs
> 
> One of the cui that I need to get is for Bactria like " Enterococcus faecium"
> but I am not seeing it. I am writing a new annotator to get those cui 
> and save them in a map. Do you have any applicationContext that I can 
> save those values and retrieve them in my annotators which are at the 
> end of the pipeline or I should use something like ehcache?
> 
> 
> -----Original Message-----
> From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> Sent: Tuesday, July 08, 2014 3:56 PM
> To: 'dev@ctakes.apache.org'
> Subject: RE: Retrieving CUIs
> 
> In your CAS, I see
> 
> <textsem:ProcedureMention xmi:id="585" sofa="1" begin="0" end="13"
> id="0" ontologyConceptArr="550 564 543 557 571"
> 
> Reading the CAS xmi, to see the first element in the array, we look 
> for ID 550, which takes us to
> 
> <refsem:UmlsConcept xmi:id="550" codingScheme="SNOMED"
> code="168335002" cui="C0430404" tui="T059"/>
> 
> So it seems like whatever you are doing to try to read out the CUI is 
> not accessing something correctly.
> 
> -- James
> 
> -----Original Message-----
> From: Nick Nikandish [mailto:snikandi@emerginghealthit.com]
> Sent: Tuesday, July 08, 2014 2:46 PM
> To: dev@ctakes.apache.org
> Subject: RE: Retrieving CUIs
> 
> Sure:
> 
> <?xml version="1.0" encoding="UTF-8"?><xmi:XMI 
> xmlns:refsem="http:///org/apache/ctakes/typesystem/type/refsem.ecore"
> xmlns:type4="http:///org/apache/ctakes/padtermspotter/type.ecore"
> xmlns:cas="http:///uima/cas.ecore"
> xmlns:types3="http:///org/montefiore/cri/nlp/culturetests/uima/types.e
> cor
> e"
> xmlns:type6="http:///org/apache/ctakes/smokingstatus/i2b2/type.ecore"
> xmlns:util="http:///org/apache/ctakes/typesystem/type/util.ecore"
> xmlns:types="http:///org/apache/ctakes/assertion/medfacts/types.ecore"
> xmlns:type="http:///org/apache/ctakes/constituency/parser/uima/type.ec
> o re" xmlns:tcas="http:///uima/tcas.ecore"
> xmlns:type2="http:///org/apache/ctakes/coreference/type.ecore"
> xmlns:types2="http:///org/apache/ctakes/assertion/zoner/types.ecore"
> xmlns:type7="http:///org/apache/ctakes/smokingstatus/type.ecore"
> xmlns:syntax="http:///org/apache/ctakes/typesystem/type/syntax.ecore"
> xmlns:type5="http:///org/apache/ctakes/sideeffect/type.ecore"
> xmlns:xmi="http://www.omg.org/XMI"
> xmlns:textspan="http:///org/apache/ctakes/typesystem/type/textspan.eco
> re"
> xmlns:assertion="http:///org/apache/ctakes/typesystem/type/temporary/a
> ssertion.ecore"
> xmlns:structured="http:///org/apache/ctakes/typesystem/type/structured.
> ecore"
> xmlns:relation="http:///org/apache/ctakes/typesystem/type/relation.eco
> re
> "
> xmlns:textsem="http:///org/apache/ctakes/typesystem/type/textsem.ecor
> e" xmlns:type3="http:///org/apache/ctakes/drugner/type.ecore"
> xmlns:libsvm="http:///org/apache/ctakes/smokingstatus/type/libsvm.ecor
> e " xmlns:type8="http:///org/apache/ctakes/typesystem/type.ecore"
> xmi:version="2.0"><cas:NULL xmi:id="0"/><cas:Sofa xmi:id="1"
> sofaNum="1" sofaID="_InitialView" mimeType="text/plain"
> sofaString="urine culture mos source/body site clean catch culture 
> results &gt;100,001col/ml escherichia coli final id e.coli amikacin s 
> ampicillin r &gt;=32 &#13;&#10;"/><cas:Sofa xmi:id="13" sofaNum="2"
sofaID="UriView"
> sofaURI="file:/C:/srv/apps/nlp/testdata/tmp.txt"/><tcas:DocumentAnnota
> ti on xmi:id="8" sofa="1" begin="0" end="142" language="x- 
> unspecified"/><textspan:Segment xmi:id="20" sofa="1" begin="0"
> end="142" id="SIMPLE_SEGMENT"/><textspan:Sentence xmi:id="26"
> sofa="1" begin="0" end="139"
> sentenceNumber="0"/><syntax:NewlineToken xmi:id="32" sofa="1"
> begin="140" end="142" tokenNumber="30"/><syntax:WordToken
> xmi:id="40" sofa="1" begin="0" end="5" tokenNumber="0"
> partOfSpeech="NN" capitalization="0" numPosition="0"
> canonicalForm="urine"/><syntax:WordToken xmi:id="52" sofa="1"
> begin="6" end="13" tokenNumber="1" partOfSpeech="NN"
> capitalization="0" numPosition="0"
> canonicalForm="culture"/><syntax:WordToken xmi:id="64" sofa="1"
> begin="14" end="17" tokenNumber="2" partOfSpeech="NNS"
> capitalization="0" numPosition="0"
> canonicalForm="mos"/><syntax:WordToken xmi:id="76" sofa="1"
> begin="18" end="24" tokenNumber="3" partOfSpeech="NN"
> capitalization="0" numPosition="0"
> canonicalForm="source"/><syntax:WordToken xmi:id="96" sofa="1"
> begin="25" end="29" tokenNumber="5" partOfSpeech="NN"
> capitalization="0" numPosition="0"
> canonicalForm="body"/><syntax:WordToken xmi:id="108" sofa="1"
> begin="30" end="34" tokenNumber="6" partOfSpeech="NN"
> capitalization="0" numPosition="0"
> canonicalForm="site"/><syntax:WordToken xmi:id="120" sofa="1"
> begin="35" end="40" tokenNumber="7" partOfSpeech="JJ"
> capitalization="0" numPosition="0"
> canonicalForm="clean"/><syntax:WordToken xmi:id="132" sofa="1"
> begin="41" end="46" tokenNumber="8" partOfSpeech="NN"
> capitalization="0" numPosition="0"
> canonicalForm="catch"/><syntax:WordToken xmi:id="144" sofa="1"
> begin="47" end="54" tokenNumber="9" partOfSpeech="NN"
> capitalization="0" numPosition="0"
> canonicalForm="culture"/><syntax:WordToken xmi:id="156" sofa="1"
> begin="55" end="62" tokenNumber="10" partOfSpeech="NNS"
> capitalization="0" numPosition="0"
> canonicalForm="result"/><syntax:WordToken xmi:id="185" sofa="1"
> begin="71" end="74" tokenNumber="13" partOfSpeech="NN"
> capitalization="0" numPosition="0"
> canonicalForm="col"/><syntax:WordToken xmi:id="205" sofa="1"
> begin="75" end="77" tokenNumber="15" partOfSpeech="NN"
> capitalization="0" numPosition="0"
> canonicalForm="ml"/><syntax:WordToken xmi:id="217" sofa="1" begin="78"
> end="89" tokenNumber="16" partOfSpeech="NN" capitalization="0"
> numPosition="0" canonicalForm="escherichia"/><syntax:WordToken
> xmi:id="229" sofa="1" begin="90" end="94" tokenNumber="17"
> partOfSpeech="NN" capitalization="0" numPosition="0"
> canonicalForm="coli"/><syntax:WordToken xmi:id="241" sofa="1"
> begin="95" end="100" tokenNumber="18" partOfSpeech="JJ"
> capitalization="0" numPosition="0"
> canonicalForm="final"/><syntax:WordToken xmi:id="253" sofa="1"
> begin="101" end="103" tokenNumber="19" partOfSpeech="JJ"
> capitalization="0" numPosition="0"
> canonicalForm="id"/><syntax:WordToken xmi:id="265" sofa="1"
> begin="104" end="105" tokenNumber="20" partOfSpeech="NN"
> capitalization="0" numPosition="0" 
> canonicalForm="e"/><syntax:WordToken
> xmi:id="285" sofa="1" begin="106" end="110" tokenNumber="22"
> partOfSpeech="NNP" capitalization="0" numPosition="0"
> canonicalForm="coli"/><syntax:WordToken xmi:id="297" sofa="1"
> begin="111" end="119" tokenNumber="23" partOfSpeech="NN"
> capitalization="0" numPosition="0"
> canonicalForm="amikacin"/><syntax:WordToken xmi:id="309" sofa="1"
> begin="120" end="121" tokenNumber="24" partOfSpeech="NN"
> capitalization="0" numPosition="0" 
> canonicalForm="s"/><syntax:WordToken
> xmi:id="321" sofa="1" begin="122" end="132" tokenNumber="25"
> partOfSpeech="NN" capitalization="0" numPosition="0"
> canonicalForm="ampicillin"/><syntax:WordToken xmi:id="333" sofa="1"
> begin="133" end="134" tokenNumber="26" partOfSpeech="VB"
> capitalization="0" numPosition="0"
> canonicalForm="r"/><syntax:PunctuationToken xmi:id="88" sofa="1"
> begin="24" end="25" tokenNumber="4"
> partOfSpeech="SYM"/><syntax:PunctuationToken xmi:id="168" sofa="1"
> begin="63" end="64" tokenNumber="11"
> partOfSpeech="SYM"/><syntax:PunctuationToken xmi:id="197" sofa="1"
> begin="74" end="75" tokenNumber="14"
> partOfSpeech="SYM"/><syntax:PunctuationToken xmi:id="277" sofa="1"
> begin="105" end="106" tokenNumber="21"
> partOfSpeech="."/><syntax:PunctuationToken xmi:id="345" sofa="1"
> begin="135" end="136" tokenNumber="27"
> partOfSpeech="SYM"/><syntax:NumToken xmi:id="176" sofa="1"
> begin="64" end="71" tokenNumber="12" partOfSpeech="CD"
> numType="1"/><syntax:NumToken xmi:id="361" sofa="1" begin="137"
> end="139" tokenNumber="29" partOfSpeech="CD"
> numType="1"/><syntax:SymbolToken xmi:id="353" sofa="1" begin="136"
> end="137" tokenNumber="28"
> partOfSpeech="SYM"/><textsem:RomanNumeralAnnotation xmi:id="370"
> sofa="1" begin="75" end="77" id="0" typeID="0" discoveryTechnique="0"
> confidence="0.0" polarity="0" uncertainty="0" conditional="false"
> generic="false" historyOf="0"/><textsem:RomanNumeralAnnotation
> xmi:id="388" sofa="1" begin="101" end="103" id="0" typeID="0"
> discoveryTechnique="0" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" generic="false" historyOf="0"/><syntax:NP xmi:id="406"
> sofa="1" begin="0" end="24" chunkType="NP"/><syntax:NP xmi:id="416"
> sofa="1" begin="25" end="62" chunkType="NP"/><syntax:NP xmi:id="426"
> sofa="1" begin="64" end="74" chunkType="NP"/><syntax:NP xmi:id="436"
> sofa="1" begin="75" end="105" chunkType="NP"/><syntax:NP xmi:id="446"
> sofa="1" begin="106" end="132" chunkType="NP"/><syntax:NP xmi:id="456" 
> sofa="1" begin="135" end="136"
> chunkType="NP"/><syntax:NP xmi:id="461" sofa="1" begin="136"
> end="137" chunkType="NP"/><syntax:NP xmi:id="466" sofa="1"
> begin="137" end="139" chunkType="NP"/><syntax:O xmi:id="411" sofa="1"
> begin="24" end="25" chunkType="O"/><syntax:O xmi:id="421" sofa="1"
> begin="63" end="64" chunkType="O"/><syntax:O xmi:id="431" sofa="1"
> begin="74" end="75" chunkType="O"/><syntax:O xmi:id="441" sofa="1"
> begin="105" end="106" chunkType="O"/><syntax:VP xmi:id="451" sofa="1"
> begin="133" end="134"
> chunkType="VP"/><textspan:LookupWindowAnnotation xmi:id="471"
> sofa="1" begin="0" end="24"/><textspan:LookupWindowAnnotation
> xmi:id="475" sofa="1" begin="25"
> end="62"/><textspan:LookupWindowAnnotation xmi:id="479" sofa="1"
> begin="64" end="74"/><textspan:LookupWindowAnnotation xmi:id="483"
> sofa="1" begin="75" end="105"/><textspan:LookupWindowAnnotation
> xmi:id="487" sofa="1" begin="106"
> end="132"/><textspan:LookupWindowAnnotation xmi:id="491" sofa="1"
> begin="135" end="136"/><textspan:LookupWindowAnnotation xmi:id="495"
> sofa="1" begin="136" end="137"/><textspan:LookupWindowAnnotation
> xmi:id="499" sofa="1" begin="137"
> end="139"/><textsem:SignSymptomMention xmi:id="513" sofa="1"
> begin="18" end="24" id="0" ontologyConceptArr="503" typeID="3"
> discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" generic="false"
> historyOf="0"/><textsem:SignSymptomMention xmi:id="795" sofa="1"
> begin="41" end="46" id="0" ontologyConceptArr="785" typeID="3"
> discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" generic="false"
> historyOf="0"/><textsem:ProcedureMention xmi:id="585" sofa="1"
> begin="0" end="13" id="0" ontologyConceptArr="550 564 543 557 571"
> typeID="5" discoveryTechnique="1" confidence="0.0" polarity="0"
> uncertainty="0" conditional="false" generic="false"
> historyOf="0"/><textsem:ProcedureMention xmi:id="671" sofa="1"
> begin="6" end="13" id="0" ontologyConceptArr="627 655 648 613 634 641 
> 620" typeID="5" discoveryTechnique="1" confidence="0.0" polarity="0"
> uncertainty="0" conditional="false" generic="false"
> historyOf="0"/><textsem:ProcedureMention xmi:id="757" sofa="1"
> begin="47" end="54" id="0" ontologyConceptArr="713 699 734 720 706 741 
> 727" typeID="5" discoveryTechnique="1" confidence="0.0" polarity="0"
> uncertainty="0" conditional="false" generic="false"
> historyOf="0"/><textsem:MedicationMention xmi:id="851" sofa="1"
> begin="78" end="94" id="0" ontologyConceptArr="828" typeID="1"
> discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" generic="false"
> historyOf="0"/><textsem:MedicationMention xmi:id="907" sofa="1"
> begin="122" end="132" id="0" ontologyConceptArr="884" typeID="1"
> discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" generic="false"
> historyOf="0"/><textsem:MedicationMention xmi:id="963" sofa="1"
> begin="111" end="119" id="0" ontologyConceptArr="940" typeID="1"
> discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" generic="false" historyOf="0"/><types3:CultureTest
> xmi:id="993" sofa="1" begin="0" end="142"
> antibiogramAnalysisProcedure="1049 1066" specimen="1141"
> bacterialColonySize="1008"
> uri="http://ric.einstein.yu.edu/im_culture_test#UrineCultureTest__113c
> a0c
> 0-2c4c-4b9e-9ca5-6f3a6b73bf1e"
> correspondsTo="http://ric.einstein.yu.edu/terminology#EscherichiaColiD
> NA ACnc" valueOf="http://ric.einstein.yu.edu/terminology#CultureTest"
> sofaString="urine culture mos source/body site clean catch culture 
> results &gt;100,001col/ml escherichia coli final id e.coli amikacin s 
> ampicillin r &gt;=32 &#13;&#10;" 
> text="EscherichiaColi"/><types3:BacterialColonySize
> xmi:id="1008" sofa="1" begin="63" end="94" criValue="100,001"
> arithmeticOperators="1024" criFloatValue="100001.0" unitConcept="1036"
> uri="http://ric.einstein.yu.edu/im_culture_test#BacterialColonySize__2
> 0ea8
> e04-cf15-4d68-b351-a04c92a322a6"
> correspondsTo="http://ric.einstein.yu.edu/terminology#FloatRules"
> valueOf="http://ric.einstein.yu.edu/terminology#BacterialColonySize"
> sofaString="&gt;100,001col/ml escherichia coli"
> text="FloatRules"/><types3:ArithmeticOperators xmi:id="1024" sofa="1"
> begin="63" end="64"
> uri="http://ric.einstein.yu.edu/im_culture_test#Greater__0ec42e0f-63b1
> -
> 40b2-842f-eb09706b52c1"
> correspondsTo="http://ric.einstein.yu.edu/im_culture_test#Greater"
> valueOf="http://ric.einstein.yu.edu/terminology#ArithmeticOperators"
> sofaString="&gt;" text="Greater"/><types3:ArithmeticOperators
> xmi:id="1105" sofa="1" begin="135" end="137"
> uri="http://ric.einstein.yu.edu/terminology#ArithmeticOperators___deaa
> 90
> 82-33ff-4be5-b7c1-f20ee60922e8"
> correspondsTo="http://ric.einstein.yu.edu/im_culture_test#LessEqual"
> valueOf="http://ric.einstein.yu.edu/terminology#ArithmeticOperators"
> sofaString="&gt;=" text="LessEqual"/><types3:UnitConcept xmi:id="1036"
> sofa="1" begin="71" end="77"
> uri="http://ric.einstein.yu.edu/im_culture_test#ColPerMl__da5a75df-27c
> 3-
> 49a0-a432-fb24eeb66a96"
> correspondsTo="http://ric.einstein.yu.edu/im_culture_test#ColPerMl"
> valueOf="http://ric.einstein.yu.edu/terminology#UnitConcept"
> sofaString="col/ml"
> text="ColPerMl"/><types3:AntibiogramAnalysisProcedure xmi:id="1049"
> sofa="1" begin="111" end="122" antibioticSensitivity="1117"
> antibodyTiter="0"
> uri="http://ric.einstein.yu.edu/im_culture_test#types__da56099c-1b7c-
> 46a4-b364-726464b0ae5b"
> correspondsTo="http://montefiore.org/umls/mth#MIC"
> valueOf="http://ric.einstein.yu.edu/terminology#AntibiogramAnalysisPro
> ce dure" sofaString="amikacin s " text="AmikacinSusceptibility"
> ontologyConcept="1061"/><types3:AntibiogramAnalysisProcedure
> xmi:id="1066" sofa="1" begin="122" end="139" antibioticSensitivity="1129"
> antibodyTiter="1090 0"
> uri="http://ric.einstein.yu.edu/im_culture_test#types__6d80da49-29a8-
> 430c-8ae6-871e78659031"
> correspondsTo="http://montefiore.org/umls/mth#MIC"
> valueOf="http://ric.einstein.yu.edu/terminology#AntibiogramAnalysisPro
> ce dure" sofaString="ampicillin r &gt;=32" 
> text="AmpicillinSusceptibility"
> ontologyConcept="1078"/><types3:AntibodyTiter xmi:id="1090" sofa="1"
> begin="135" end="139" criValue="32" arithmeticOperators="1105"
> criFloatValue="32.0"
> uri="http://ric.einstein.yu.edu/im_culture_test#AntibodyTiter__f3242ae
> b-
> 88fb-417c-8446-b180af943235"
> correspondsTo="http://ric.einstein.yu.edu/terminology#FloatRules"
> valueOf="http://ric.einstein.yu.edu/terminology#AntibodyTiter"
> sofaString="&gt;=32" text="FloatRules"/><types3:AntibioticSensitivity
> xmi:id="1117" sofa="1" begin="120" end="121"
> uri="http://ric.einstein.yu.edu/im_culture_test#AntibioticSensitivity_
> _6e7e
> 76c3-3c00-43fb-925c-43b2fb239414"
> correspondsTo="http://ric.einstein.yu.edu/terminology#TestSensitive"
> valueOf="org.montefiore.cri.nlp.culturetests.uima.types.AntibioticSens
> itivity " sofaString="s" 
> text="TestSensitive"/><types3:AntibioticSensitivity
> xmi:id="1129" sofa="1" begin="133" end="134"
> uri="http://ric.einstein.yu.edu/im_culture_test#AntibioticSensitivity_
> _7e1b
> 2074-e396-447f-95d9-b6eefe6ea730"
> correspondsTo="http://ric.einstein.yu.edu/terminology#TestResistant"
> valueOf="org.montefiore.cri.nlp.culturetests.uima.types.AntibioticSens
> itivity " sofaString="r" text="TestResistant"/><types3:Specimen 
> xmi:id="1141"
> sofa="1" begin="0" end="62" specimenSource="1177" biologicalType="1168"
> uri="http://ric.einstein.yu.edu/im_culture_test#Specimen__fd5bcc82-5ea
> 5-
> 4d73-87e6-c7cc6dc660b7"
> correspondsTo="http://ric.einstein.yu.edu/terminology#Specimen"
> valueOf="http://ric.einstein.yu.edu/terminology#Specimen"
> sofaString="urine culture mos source/body site clean catch culture results"
> text="Specimen"/><types3:BiologicalType xmi:id="1168" sofa="1" begin="0"
> end="5"
> uri="http://ric.einstein.yu.edu/im_culture_test#BiologicalType__bf502c
> 06-
> 043c-4c53-ab79-a3c37972c404"
> correspondsTo="http://ric.einstein.yu.edu/terminology#Urine"
> valueOf="http://ric.einstein.yu.edu/terminology#BiologicalType"
> sofaString="urine" text="Urine"/><types3:SpecimenSource xmi:id="1177"
> sofa="1" begin="35" end="46"
> uri="http://ric.einstein.yu.edu/im_culture_test#SpecimenSource__d932f1
> 0
> 2-e3cf-4022-a7fc-0b1a6695d102"
> correspondsTo="http://ric.einstein.yu.edu/terminology#CleanCatch"
> valueOf="http://ric.einstein.yu.edu/terminology#SpecimenSource"
> sofaString="clean catch" text="CleanCatch"/><types3:OntologyConcept
> xmi:id="1078" codingScheme="RXNORM"
> code="C0002680"/><types3:OntologyConcept xmi:id="1061"
> codingScheme="RXNORM" code="C0002499"/><refsem:OntologyConcept
> xmi:id="940" codingScheme="RXNORM"
> code="C0002499"/><refsem:OntologyConcept xmi:id="884"
> codingScheme="RXNORM" code="C0002680"/><refsem:OntologyConcept
> xmi:id="828" codingScheme="RXNORM"
> code="C0014834"/><refsem:UmlsConcept xmi:id="727"
> codingScheme="SNOMED" code="145414005" cui="C0430400"
> tui="T059"/><refsem:UmlsConcept xmi:id="741" codingScheme="SNOMED"
> code="252397004" cui="C0430400" tui="T059"/><refsem:UmlsConcept 
> xmi:id="706" codingScheme="SNOMED" code="252398009" cui="C0430400"
> tui="T059"/><refsem:UmlsConcept xmi:id="720" codingScheme="SNOMED"
> code="168185003" cui="C0430400" tui="T059"/><refsem:UmlsConcept 
> xmi:id="734" codingScheme="SNOMED" code="270035009" cui="C0430400"
> tui="T059"/><refsem:UmlsConcept xmi:id="699" codingScheme="SNOMED"
> code="61594008" cui="C2242979" tui="T059"/><refsem:UmlsConcept 
> xmi:id="713" codingScheme="SNOMED" code="145422003" cui="C0430400"
> tui="T059"/><refsem:UmlsConcept xmi:id="620" codingScheme="SNOMED"
> code="252398009" cui="C0430400" tui="T059"/><refsem:UmlsConcept 
> xmi:id="641" codingScheme="SNOMED" code="145414005" cui="C0430400"
> tui="T059"/><refsem:UmlsConcept xmi:id="634" codingScheme="SNOMED"
> code="168185003" cui="C0430400" tui="T059"/><refsem:UmlsConcept 
> xmi:id="613" codingScheme="SNOMED" code="61594008" cui="C2242979"
> tui="T059"/><refsem:UmlsConcept xmi:id="648" codingScheme="SNOMED"
> code="270035009" cui="C0430400" tui="T059"/><refsem:UmlsConcept 
> xmi:id="655" codingScheme="SNOMED" code="252397004" cui="C0430400"
> tui="T059"/><refsem:UmlsConcept xmi:id="627" codingScheme="SNOMED"
> code="145422003" cui="C0430400" tui="T059"/><refsem:UmlsConcept 
> xmi:id="571" codingScheme="SNOMED" code="145543000" cui="C0430404"
> tui="T059"/><refsem:UmlsConcept xmi:id="557" codingScheme="SNOMED"
> code="144792004" cui="C0430404" tui="T059"/><refsem:UmlsConcept 
> xmi:id="543" codingScheme="SNOMED" code="117010004" cui="C0430404"
> tui="T059"/><refsem:UmlsConcept xmi:id="564" codingScheme="SNOMED"
> code="275885001" cui="C0430404" tui="T059"/><refsem:UmlsConcept 
> xmi:id="550" codingScheme="SNOMED" code="168335002" cui="C0430404"
> tui="T059"/><refsem:UmlsConcept xmi:id="785" codingScheme="SNOMED"
> code="30623001" cui="C0231617" tui="T184"/><refsem:UmlsConcept 
> xmi:id="503" codingScheme="SNOMED" code="260753009" cui="C0449416"
> tui="T033"/><cas:View sofa="1" members="8 20 26 32 40 52 64 76 96 108 
> 120
> 132 144 156 185 205 217 229 241 253 265 285 297 309 321 333 88 168 197 
> 277 345
> 176 361 353 370 388 406 416 426 436 446 456 461 466 411 421 431 441 
> 451 471
> 475 479 483 487 491 495 499 513 795 585 671 757 851 907 963 993 1008 
> 1024
> 1105 1036 1049 1066 1090 1117 1129 1141 1168 1177"/><cas:View 
> sofa="13"/></xmi:XMI>
> 
> 
> 
> 
> 
> -----Original Message-----
> From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> Sent: Tuesday, July 08, 2014 3:44 PM
> To: 'dev@ctakes.apache.org'
> Subject: RE: Retrieving CUIs
> 
> The attachment didn't come through so if the other email I sent didn't 
> help, please post the xmi somewhere that I can download it from. Thanks.
> 
> -----Original Message-----
> From: Nick Nikandish [mailto:snikandi@emerginghealthit.com]
> Sent: Tuesday, July 08, 2014 2:14 PM
> To: dev@ctakes.apache.org
> Subject: RE: Retrieving CUIs
> 
> The xmi file is attached.
> 
> 
> -----Original Message-----
> From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> Sent: Tuesday, July 08, 2014 2:54 PM
> To: 'dev@ctakes.apache.org'
> Subject: RE: Retrieving CUIs
> 
> What gets annotated depends on which pipeline you use.
> The pipeline mentioned in the User Guide should also annotate 
> diseases/disorders, signs/symptoms, procedures, and anatomical sites. 
> So first would be to check which pipeline you are using.
> 
> Or perhaps you do not have the separately downloadable dictionary. To 
> test that, try text that includes the words "knee" and "pain". If 
> those are annotated and other anatomical sites and signs/symptoms are 
> not, you probably don't have the dictionary resources or don't have 
> them on your classpath.
> 
> Good things to post to help us help you are:
>  - whether you are using CVD or CPE GUI, or a program/script
>  - the name of pipeline you are running (are you loading an XML 
> descriptor into CVD or CPE), or the name of the script/program
>  - a sample output file (xcas/xmi) [make sure not to include any PHI 
> in the sample text that you process if you are going to post the 
> output]
> 
> -- James
> 
> -----Original Message-----
> From: Nick Nikandish [mailto:snikandi@emerginghealthit.com]
> Sent: Tuesday, July 08, 2014 1:43 PM
> To: dev@ctakes.apache.org
> Subject: Retrieving CUIs
> 
> Hi there,
> 
> I was wondering if there is any way to retrieve CUIs for the tokens of 
> a free text in CTakes without changing the codebase? I am able to 
> retrieve CUIs for only medications  in a text.
> 
> 
> 
> Thanks,
> Nick
> 


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