2017
Finding useful data across multiple biomedical data repositories using DataMed
Ohno-Machado L, Sansone S, Alter G, Fore I, Grethe J, Xu H, Gonzalez-Beltran A, Rocca-Serra P, Gururaj A, Bell E, Soysal E, Zong N, Kim H. Finding useful data across multiple biomedical data repositories using DataMed. Nature Genetics 2017, 49: 816-819. PMID: 28546571, PMCID: PMC6460922, DOI: 10.1038/ng.3864.Peer-Reviewed Original ResearchMeSH KeywordsBiological OntologiesBiomedical ResearchComputational BiologyDatabases, FactualHumansMetadataSoftwareSystems IntegrationConceptsBiomedical data repositoriesHealth big dataData setsKnowledge discoveryBig dataMultiple repositoriesSearch enginesData indexFAIR principlesDataMedData repositoryService providersKnowledge initiativesKnowledge expertsBiomedical research communityResearch communityRepositoryScience landscapeUseful dataInteroperabilityMetadataFindabilitySetEngineData
2011
Data from clinical notes: a perspective on the tension between structure and flexible documentation
Rosenbloom S, Denny J, Xu H, Lorenzi N, Stead W, Johnson K. Data from clinical notes: a perspective on the tension between structure and flexible documentation. Journal Of The American Medical Informatics Association 2011, 18: 181-186. PMID: 21233086, PMCID: PMC3116264, DOI: 10.1136/jamia.2010.007237.Peer-Reviewed Original ResearchConceptsReusable dataElectronic health record system adoptionStructured documentationComputer-based documentation systemsClinical notesClinical documentationStructured dataText processingSystem adoptionRecord systemSuch systemsDocumentation systemWorkflowContent needsProvidersUsabilityDocumentationExpressivitySystemHealthcare providersPatient careDataProcessingMajor goalAdoption
2010
Integrating existing natural language processing tools for medication extraction from discharge summaries
Doan S, Bastarache L, Klimkowski S, Denny J, Xu H. Integrating existing natural language processing tools for medication extraction from discharge summaries. Journal Of The American Medical Informatics Association 2010, 17: 528-531. PMID: 20819857, PMCID: PMC2995674, DOI: 10.1136/jamia.2010.003855.Peer-Reviewed Original Research
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