2015
Ease of adoption of clinical natural language processing software: An evaluation of five systems
Zheng K, Vydiswaran V, Liu Y, Wang Y, Stubbs A, Uzuner Ö, Gururaj A, Bayer S, Aberdeen J, Rumshisky A, Pakhomov S, Liu H, Xu H. Ease of adoption of clinical natural language processing software: An evaluation of five systems. Journal Of Biomedical Informatics 2015, 58: s189-s196. PMID: 26210361, PMCID: PMC4974203, DOI: 10.1016/j.jbi.2015.07.008.Peer-Reviewed Original ResearchMeSH KeywordsAttitude to ComputersData MiningElectronic Health RecordsHumansMiddle AgedNatural Language ProcessingPattern Recognition, AutomatedSoftwareUser-Computer InterfaceConceptsClinical NLP systemsNLP systemsNatural language processing softwareThird-party componentsUsability testing toolGroup of usersLanguage processing softwareEase of adoptionExpert evaluatorsSoftware distributionBiomedical softwareComputer scienceEnd usersUsability assessmentI2b2 challengeTesting toolsEvaluation showHuman evaluatorsSystem submissionsEase of useHealth informaticsProcessing softwareAdoption issuesUsersSpecial trackA Preliminary Study of Clinical Abbreviation Disambiguation in Real Time
Wu Y, Denny J, Rosenbloom S, Miller R, Giuse D, Song M, Xu H. A Preliminary Study of Clinical Abbreviation Disambiguation in Real Time. Applied Clinical Informatics 2015, 06: 364-374. PMID: 26171081, PMCID: PMC4493336, DOI: 10.4338/aci-2014-10-ra-0088.Peer-Reviewed Original ResearchMeSH KeywordsAbbreviations as TopicDocumentationHealth PersonnelNatural Language ProcessingTime FactorsUser-Computer InterfaceConceptsElectronic health record systemsUser studyClinical documentation systemNatural language processing systemsClinical NLP systemsPreliminary user studyAbbreviation recognitionExtra time costLanguage processing systemWSD methodHealth record systemsDocumentation systemPrototype applicationWord sense disambiguation methodNLP systemsCorrect sensesNote generationPrototype systemClinical sentencesCost of timeClinical documentsDocument entryDisambiguation moduleSense disambiguation methodHealthcare records
2012
Identifying the status of genetic lesions in cancer clinical trial documents using machine learning
Wu Y, Levy M, Micheel C, Yeh P, Tang B, Cantrell M, Cooreman S, Xu H. Identifying the status of genetic lesions in cancer clinical trial documents using machine learning. BMC Genomics 2012, 13: s21. PMID: 23282337, PMCID: PMC3535695, DOI: 10.1186/1471-2164-13-s8-s21.Peer-Reviewed Original ResearchDTome: a web-based tool for drug-target interactome construction
Sun J, Wu Y, Xu H, Zhao Z. DTome: a web-based tool for drug-target interactome construction. BMC Bioinformatics 2012, 13: s7. PMID: 22901092, PMCID: PMC3372450, DOI: 10.1186/1471-2105-13-s9-s7.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsClozapineComputational BiologyDatabases, FactualDrug DiscoveryDrug InteractionsHumansInternetProteinsSoftwareUser-Computer InterfaceConceptsWeb-based toolUser-friendly web interfaceWeb-based queriesRich data sourceDifferent knowledge basesDatabase schemaWeb interfaceVisualization processKnowledge basesComputational workflowDiscovery processData sourcesNetworkDrug-target interactionsDrugs' primary targetsDrug-target networkWorkflowEarly-stage drug discoveryNetwork analysisQueriesToolPromising approachDrug discovery processSchemaDetailed network analysis
2006
Natural language processing and visualization in the molecular imaging domain
Tulipano P, Tao Y, Millar W, Zanzonico P, Kolbert K, Xu H, Yu H, Chen L, Lussier Y, Friedman C. Natural language processing and visualization in the molecular imaging domain. Journal Of Biomedical Informatics 2006, 40: 270-281. PMID: 17084109, DOI: 10.1016/j.jbi.2006.08.002.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell LineComputational BiologyDatabases, BibliographicDatabases, GeneticDiagnostic ImagingGenomicsHumansInformation Storage and RetrievalNatural Language ProcessingPhenotypeProgramming LanguagesSoftwareSystems IntegrationTerminology as TopicUser-Computer InterfaceVocabulary, ControlledConceptsImaging domainNatural language processing systemsNatural language processingLanguage processing systemJava viewerNLP systemsFormal evaluation studiesLanguage processingInformation resourcesProcessing systemMedical imagingIndex imagesSystem performanceBiological informationInformationImagesVisualizationBioMedLEEPerformanceNLPEvaluation studyDomainGenomics literatureSystemSimultaneous visualization