2017
CLAMP – a toolkit for efficiently building customized clinical natural language processing pipelines
Soysal E, Wang J, Jiang M, Wu Y, Pakhomov S, Liu H, Xu H. CLAMP – a toolkit for efficiently building customized clinical natural language processing pipelines. Journal Of The American Medical Informatics Association 2017, 25: 331-336. PMID: 29186491, PMCID: PMC7378877, DOI: 10.1093/jamia/ocx132.Peer-Reviewed Original ResearchGraphic user interfaceUser interfaceUser-friendly graphic user interfaceNatural language processing systemsClinical natural language processing (NLP) systemsNatural language processing pipelineKnowledge Extraction SystemLanguage processing pipelineClinical Text AnalysisLanguage processing systemNLP componentsNLP toolkitInformation extractionNLP pipelineUse casesEntity recognitionClinical textEnd usersNLP communityProcessing pipelineProcessing systemIndividual tasksIndividual applicationsText analysisBetter performance
2016
A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD)
Wu Y, Denny J, Rosenbloom S, Miller R, Giuse D, Wang L, Blanquicett C, Soysal E, Xu J, Xu H. A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD). Journal Of The American Medical Informatics Association 2016, 24: e79-e86. PMID: 27539197, PMCID: PMC7651947, DOI: 10.1093/jamia/ocw109.Peer-Reviewed Original ResearchConceptsClinical NLP systemsOpen-source frameworkNLP systemsClinical corpusClinical abbreviationsClinic visit notesSense inventoryKnowledge Extraction SystemAbbreviation recognitionWord sense disambiguation methodDischarge summariesF1 scoreExternal corpusClinical narrativesSense disambiguation methodSystem capabilitiesVanderbilt University Medical CenterWrapperFrequent abbreviationsDisambiguation methodMetaMapAbbreviation identificationCardsVisit notesDisambiguation
2012
A study of transportability of an existing smoking status detection module across institutions.
Liu M, Shah A, Jiang M, Peterson N, Dai Q, Aldrich M, Chen Q, Bowton E, Liu H, Denny J, Xu H. A study of transportability of an existing smoking status detection module across institutions. AMIA Annual Symposium Proceedings 2012, 2012: 577-86. PMID: 23304330, PMCID: PMC3540509.Peer-Reviewed Original ResearchConceptsDetection moduleNatural language processing systemsKnowledge Extraction SystemEMR dataRule-based classifierClinical Text AnalysisHighest F-measureLanguage processing systemElectronic medical recordsF-measureLevels of classificationProcessing systemSpecific tasksText analysisClassifierDesirable performanceModuleModest effortExtraction systemCTAKESSmoking moduleMachineSystemTaskClassification