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.ecore"; 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.ecore"; 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.ecore"; xmlns:assertion="http:///org/apache/ctakes/typesystem/type/temporary/assertion.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.ecore"; 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:DocumentAnnotation 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__113ca0c0-2c4c-4b9e-9ca5-6f3a6b73bf1e"; correspondsTo="http://ric.einstein.yu.edu/terminology#EscherichiaColiDNAACnc"; 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__20ea8e04-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___deaa9082-33ff-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#AntibiogramAnalysisProcedure"; sofaString="amikacin s " text="AmikacinSusceptibility" ontologyConcept="1061"/><types3:AntibiogramAnalysisProcedure xmi:id="1066" sofa="1" begin="122" end="139" antibioticSensitivity="1129" antibodyTiter="1090 0" 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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__d932f102-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
