ADESSA AMIA Presentation Jon Duke
Transcript of ADESSA AMIA Presentation Jon Duke
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ADESSA:AReal-TimeDecisionSupport
ServiceforDeliveryofSemancally
CodedAdverseDrugEventData
JonD.Duke,MD
AMIAAnnualSymposium2010
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Overview
Introduc@ontoADESSA ConceptandDesign Evalua@onStudy ResultsDiscussion/FutureWork
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ADESSAisawebservicedesignedto
providelabeledadversedrugeventdata
incoded,structuredform
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OriginsofADESSA
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TheProblem
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Whataboutthe
StructuredProductLabel?
CentralandPeripheralNervousSystemDisorders
Frequent: hypertonia,hypoesthesia;Infrequent:twitching,confusion,hyperkinesia,vergo,ataxia,
migraine,abnormalcoordinaon,hyperesthesia,legcramps,abnormalgait,nystagmus,
hypokinesia;Rare:dysphonia,coma,dyskinesia,
hypotonia,ptosis,choreoathetosis,hyporeflexia.
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OpenSourcesofCoded
AdverseEventData NDFRT
Physiologiceffects SIDER
CO-STARTTerminologyLimiteddrugsetInfrequentlyupdated
AdverseEventRepor@ngSystemSpontaneousreports,notlabeleddata
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Op@malSolu@on
ComprehensivesourceoflabledADEdata MedDRAcoded
usefulforpharmacovigilance/ADErepor@ngnaturalphrasingsofadverseevents,human-readable
SNOMED-CTcodedusefulforintegra@onwithclinicaldecisionsupport
Webservicecapableofretrievingdataforoneormoredrugsusingstandardmedica@oniden@fiers
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SystemComponents
StructuredProductLabelInforma@onCoderandExtractoR(SPLICER)
Quan@ta@veAdverseReac@onKnowledgebase(QuARK) AdverseDrugEventSupportService(ADESSA)
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GeneralOverviewofSPLICERArchitecture
Processors
List
MedDRA term identifier
Table
Section Extraction
XML tag removal
Text Normalization
Sentence Detection
Processors
ExactMatch
Synonym
StopStemTransform
Similarity
Tokenizer
LaboratoryMapper
SPL
~~~~~~~~~~
~~~~~~~~~~
~~~~~~~~
SPL Parser
ADE
ExtractorMedDRA
Mapping
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GeneralOverviewofSPLICERArchitecture
Processors
List
MedDRA term identifier
Table
Section Extraction
XML tag removal
Text Normalization
Sentence Detection
Processors
ExactMatch
Synonym
StopStemTransform
Similarity
Tokenizer
LaboratoryMapper
SPL~~~~~~~~~~
~~~~~~~~~~
~~~~~~~~
SPL Parser
ADE
ExtractorMedDRA
Mapping
StructuredProductLabel
XMLDocument
HL7V3Specifica@on
Mandatedsince2006
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GeneralOverviewofhowSPLICER
ProcessesSPLs
Processors
List
MedDRA term identifier
Table
Section Identification
XML tag removal
Text Normalization
Sentence Detection
Processors
ExactMatch
Synonym
StopStemTransform
Similarity
Tokenizer
LaboratoryMapper
SPL
~~~~~~~~~~
~~~~~~~~~~
~~~~~~~~
SPL Parser
ADE
ExtractorMedDRA
Mapping
Cleansandprepares
SPLforextrac@on
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GeneralOverviewofhowSPLICER
ProcessesSPLs
Processors
List
Table
MedDRA term sweeper
Section Extraction
XML tag removal
Text Normalization
Sentence Detection
Processors
ExactMatch
Synonym
StopStemTransform
Similarity
Tokenizer
LaboratoryMapper
SPL
~~~~~~~~~~
~~~~~~~~~~
~~~~~~~~
SPL Parser
ADE
Extractor MedDRAMapping
ExtractsrawADEs
fromcleanSPL
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GeneralOverviewofhowSPLICER
ProcessesSPLs
Processors
List
MedDRA term identifier
Table
Section Extraction
XML tag removal
Text Normalization
Sentence Detection
Processors
ExactMatch
Synonym
StopStem
Transform
Similarity
Tokenizer
LaboratoryMapper
SPL
~~~~~~~~~~
~~~~~~~~~~
~~~~~~~~
SPL Parser
ADE
ExtractorMedDRA
Mapping
Mapsrawtermsto
MedDRAconcepts
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DatabaseCrea@on
Retrieved5782SPLsfromDailyMed UsedSPLICERtoextractandmaptheADEsfromtheselabelstoMedDRApreferredterms
LinkedSPLstoRxCUIsusingRxNormviaSPL_SET_IDviaNDCcodes
MappedMedDRAtermstoSNOMED-CTviaUMLSCUIsynonymy
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DatabaseCrea@on
Successfullyprocessed5602SPLs180notprocessedduetoXMLvaria@on1706genericmedica@ons
Extracted545602ADEs22097uniquerawphrases8709uniqueMedDRAterms
PerLabelMeanADEs:70
MedianADEs:49Range:0to525
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ADESSA
RxCUI
String
CCD
Level3
Labeled
ADEs
ADESSAOverview
PHP/MySQL
NuSOAP
QuARK
RxCUI MedDRA
SNOMED-CT
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CCDMedica@onExample
Promethazine25MGOralTablet
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ExampleXMLResponse
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Evalua@onGoals
Assesstheaccuracyoftheadverseeventextrac@onprocess
Assessthecomprehensivenessandperformanceoftheserviceusingreal-worlddata
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NLPEvalua@on
IndependentmanualreviewofSPLICERoutputbyaMedDRAspecialist
For100randomlabels,reviewermarkedADEsTruePosiveADEinbothoutputandlabelFalsePosiveADEclaimedbySPLICERbuteither
notpresentinlabelornotatrueadverseevent
FalseNegaveADEpresentinlabelbutnotfoundbySPLICERornotcorrectlymapped
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NLPEvalua@on
Outof9529ADEs:9064TruePosi@ves
465FalsePosi@ves706FalseNega@ves
Recall:92.8%
Precision:95.1%
F-Measure:0.94
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WebServiceEvalua@on
PassedADESSA30randomlyselectedanonymizedCCDs
Measuredaccuracyofdrugcapture(howmanydrugswerecorrectlyiden@fiedandavailableinQuARK)
@mefromsubmissiontoresponse
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Results:DSS
For30CCDs,drugcountranged4-37,mean12.2 ADEssuccessfullyreturnedfor157/181(88%)ofthesedrugs
Meanresponse@me620ms Reasonsforfailuretoreturnresults(n=24)
7duetoCCDswithoutRxCUIcodes17duetoincompleteRxCUItoSPLmappingsinQuARK Innocasewasthetargetdrugmissingfromthedatabase
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Discussion
SPLICERextractedlabeledadverseeventdatawithhighprecisionandrecall
ADESSAreturnedpa@ent-specificADEdatarapidlyuponreceiptofaCCD/RxNormcodes
Poten@alvaluein:adverseeventrepor@ng(checkingagainstknownadversereac@ons)
clinicaldecisionsupport(associa@ngpa@entcondi@onswithpoten@allycausa@veagents)
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Limita@ons
Evenwith95%precision,s@ll~25,000incorrectasser@onsindatabase
Sta@csetdoesnotaccountfornewandupdatedlabels
EncounteredsomeissueswithmappingofRxCUIstoSPLs
SNOMEDconceptsmaynotreflectoriginalnuancedADEconcept
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Conclusions
Extrac@onviaNLPanddissemina@onviaDSScanprovidecodedADEdataforuseinCDS
FutureworkincludesSearchbyspecificADEorADEcategorySupportforreal-@meupdatesofQuARKusingFDAsRSSfeedfornew/updatedlabels
BroadeningofADESSAforuseoutsidefirewall
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Thanks!
Ques@ons?
JonDuke
jdukeregenstrief.org