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:[email protected]] > Sent: Tuesday, July 08, 2014 4:12 PM > To: [email protected] > 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:[email protected]] > Sent: Tuesday, July 08, 2014 3:56 PM > To: '[email protected]' > 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:[email protected]] > Sent: Tuesday, July 08, 2014 2:46 PM > To: [email protected] > 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.ecor > 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.eco > 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.ecore > " > 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.ecore > " 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 > >100,001col/ml escherichia coli final id e.coli amikacin s ampicillin r > >=32 > "/><cas:Sofa xmi:id="13" sofaNum="2" sofaID="UriView" > sofaURI="file:/C:/srv/apps/nlp/testdata/tmp.txt"/><tcas:DocumentAnnotati > 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__113ca0c > 0-2c4c-4b9e-9ca5-6f3a6b73bf1e" > correspondsTo="http://ric.einstein.yu.edu/terminology#EscherichiaColiDNA > ACnc" valueOf="http://ric.einstein.yu.edu/terminology#CultureTest"; > sofaString="urine culture mos source/body site clean catch culture results > >100,001col/ml escherichia coli final id e.coli amikacin s ampicillin r > >=32 > " 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__20ea8 > e04-cf15-4d68-b351-a04c92a322a6" > correspondsTo="http://ric.einstein.yu.edu/terminology#FloatRules"; > valueOf="http://ric.einstein.yu.edu/terminology#BacterialColonySize"; > sofaString=">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=">" text="Greater"/><types3:ArithmeticOperators > xmi:id="1105" sofa="1" begin="135" end="137" > uri="http://ric.einstein.yu.edu/terminology#ArithmeticOperators___deaa90 > 82-33ff-4be5-b7c1-f20ee60922e8" > correspondsTo="http://ric.einstein.yu.edu/im_culture_test#LessEqual"; > valueOf="http://ric.einstein.yu.edu/terminology#ArithmeticOperators"; > sofaString=">=" text="LessEqual"/><types3:UnitConcept xmi:id="1036" > sofa="1" begin="71" end="77" > uri="http://ric.einstein.yu.edu/im_culture_test#ColPerMl__da5a75df-27c3- > 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#AntibiogramAnalysisProce > 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#AntibiogramAnalysisProce > dure" sofaString="ampicillin r >=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__f3242aeb- > 88fb-417c-8446-b180af943235" > correspondsTo="http://ric.einstein.yu.edu/terminology#FloatRules"; > valueOf="http://ric.einstein.yu.edu/terminology#AntibodyTiter"; > sofaString=">=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.AntibioticSensitivity > " 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.AntibioticSensitivity > " 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__fd5bcc82-5ea5- > 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__bf502c06- > 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__d932f10 > 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:[email protected]] > Sent: Tuesday, July 08, 2014 3:44 PM > To: '[email protected]' > 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:[email protected]] > Sent: Tuesday, July 08, 2014 2:14 PM > To: [email protected] > Subject: RE: Retrieving CUIs > > The xmi file is attached. > > > -----Original Message----- > From: Masanz, James J. [mailto:[email protected]] > Sent: Tuesday, July 08, 2014 2:54 PM > To: '[email protected]' > 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:[email protected]] > Sent: Tuesday, July 08, 2014 1:43 PM > To: [email protected] > 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 >
