2009
Automated Database Mediation Using Ontological Metadata Mappings
Marenco L, Wang R, Nadkarni P. Automated Database Mediation Using Ontological Metadata Mappings. Journal Of The American Medical Informatics Association 2009, 16: 723-737. PMID: 19567801, PMCID: PMC2744723, DOI: 10.1197/jamia.m3031.Peer-Reviewed Original ResearchConceptsCross-database queriesHigh-level rulesEnforcement of constraintsDatabase MediationDatabase federationsDatabase ontologyExtended metadataGranularity levelsMetadata mappingBiomedical ontologiesDifferent granularitiesFramework simplifiesCategories of dataMaintenance of systemsMapping rulesQueriesDatabase informationGranularity of representationGlobal vocabularyOntologyGranularityIntegrator systemMetadataDatabaseSNOMED
2007
Interoperability Across Neuroscience Databases
Marenco L, Nadkarni P, Martone M, Gupta A. Interoperability Across Neuroscience Databases. Methods In Molecular Biology 2007, 401: 23-36. PMID: 18368358, DOI: 10.1007/978-1-59745-520-6_2.Peer-Reviewed Original ResearchMeSH KeywordsDatabase Management SystemsDatabases, FactualHumansInformation Storage and RetrievalNeurosciencesConceptsHuman Brain ProjectData interoperabilityData sharingNeuroscience databasesData heterogeneityCurrent data sharingSemantic data modelDatabase interoperabilityWeb servicesMetadata repositoryRobust interoperabilityMetadata annotationData integrationData modelInteroperabilityBrain ProjectInformation frameworkNeuroscience informationIntegration mechanismsSharingConstant creationDomain changesNeuroscience initiativesServicesMultidisciplinary nature
2006
Guidelines for the effective use of entity–attribute–value modeling for biomedical databases
Dinu V, Nadkarni P. Guidelines for the effective use of entity–attribute–value modeling for biomedical databases. International Journal Of Medical Informatics 2006, 76: 769-779. PMID: 17098467, PMCID: PMC2110957, DOI: 10.1016/j.ijmedinf.2006.09.023.Peer-Reviewed Original ResearchMeSH KeywordsDatabase Management SystemsEfficiency, OrganizationalGuidelines as TopicHumansMedical Informatics ApplicationsModels, OrganizationalUnited StatesInformatics tools to improve clinical research study implementation
Brandt CA, Argraves S, Money R, Ananth G, Trocky NM, Nadkarni PM. Informatics tools to improve clinical research study implementation. Contemporary Clinical Trials 2006, 27: 112-122. PMID: 16388990, DOI: 10.1016/j.cct.2005.11.013.Peer-Reviewed Original ResearchMeSH KeywordsClinical Trials as TopicComputer SecurityDatabase Management SystemsForms and Records ControlHumansInformaticsInservice Training
2005
Informatics tools to improve clinical research.
Argraves S, Brandt CA, Money R, Nadkarni P. Informatics tools to improve clinical research. AMIA Annual Symposium Proceedings 2005, 2005: 883. PMID: 16779170, PMCID: PMC1560747.Peer-Reviewed Original ResearchAutomating identification of adverse events related to abnormal lab results using standard vocabularies.
Brandt CA, Lu CC, Nadkarni PM. Automating identification of adverse events related to abnormal lab results using standard vocabularies. AMIA Annual Symposium Proceedings 2005, 2005: 903. PMID: 16779190, PMCID: PMC1560626.Peer-Reviewed Original Research
2004
VitaPad: visualization tools for the analysis of pathway data
Holford M, Li N, Nadkarni P, Zhao H. VitaPad: visualization tools for the analysis of pathway data. Bioinformatics 2004, 21: 1596-1602. PMID: 15564306, DOI: 10.1093/bioinformatics/bti153.Peer-Reviewed Original ResearchConceptsCross-platform applicationHigh-resolution graphicsGraph layout algorithmsBiological pathway diagramsPathway diagramsXML formatUser interfaceLayout algorithmVisualization toolsIntuitive controlEasy extensionPathway dataGraphicsUsersMicroarray dataAlgorithmSoftwareToolFormatDataHongyuInterfaceIntegrationPackageApplicationsQIS: A Framework for Biomedical Database Federation
Marenco L, Wang TY, Shepherd G, Miller PL, Nadkarni P. QIS: A Framework for Biomedical Database Federation. Journal Of The American Medical Informatics Association 2004, 11: 523-534. PMID: 15298995, PMCID: PMC524633, DOI: 10.1197/jamia.m1506.Peer-Reviewed Original ResearchConceptsNetwork-based serversHeterogeneous data sourcesRobust data integrationIntegration serverOntology serverDatabase federationsSource serverNeuroscience databasesData integrationMediator frameworkServerData elementsQueriesData sourcesMetadataPrototype stageStandard technologyIntegrator systemGenomic databasesFrameworkDatabaseOntologyArchitectureSchemaTechnological expertiseManaging Complex Change in Clinical Study Metadata
Brandt CA, Gadagkar R, Rodriguez C, Nadkarni PM. Managing Complex Change in Clinical Study Metadata. Journal Of The American Medical Informatics Association 2004, 11: 380-391. PMID: 15187070, PMCID: PMC516245, DOI: 10.1197/jamia.m1511.Peer-Reviewed Original ResearchMeSH KeywordsArtificial IntelligenceComputer SystemsDatabase Management SystemsDecision Support Systems, ClinicalPilot ProjectsSoftwareVocabulary, ControlledConceptsMetadata managementClinical study data management systemsHigh-level specificationData management systemProduction rule systemMiddleware enginesUse casesMetadata modificationCentralized informationStudy metadataManagement systemMetadataInformationSubschemaSystemSoftwareSpecificationEngineCapabilitySpecific typesManagementIntegration of Web-based and PC-based Clinical Research Databases
Brandt CA, Sun K, Charpentier P, Nadkarni PM. Integration of Web-based and PC-based Clinical Research Databases. Methods Of Information In Medicine 2004, 43: 287-295. PMID: 15227559, DOI: 10.1055/s-0038-1633870.Peer-Reviewed Original ResearchConceptsDatabase applicationsClinical study data management systemsIntegration of applicationsCommon semantic modelData management systemWeb-based repositoryClinical research databaseSchema conflictsSharing of featuresData managementMapping schemaSemantic modelDifferent operating environmentsModel unificationManagement systemIntegration effortsOperating environmentArea of applicabilityData collectionMajor benefitsSimilar purposesIntegrationApplicationsCritical conflictsData libraries
2003
Achieving Evolvable Web-Database Bioscience Applications Using the EAV/CR Framework: Recent Advances
Marenco L, Tosches N, Crasto C, Shepherd G, Miller PL, Nadkarni PM. Achieving Evolvable Web-Database Bioscience Applications Using the EAV/CR Framework: Recent Advances. Journal Of The American Medical Informatics Association 2003, 10: 444-453. PMID: 12807806, PMCID: PMC212781, DOI: 10.1197/jamia.m1303.Peer-Reviewed Original ResearchMeSH KeywordsDatabase Management SystemsDatabases as TopicInternetProgramming LanguagesSemanticsSoftwareVocabulary, ControlledConceptsEAV/CRXML-based protocolHuman Brain ProjectDatabase supportData querySemantic descriptorsAutomatic generationNeuroscience databasesCR frameworkScientific domainsBrain ProjectInterclass relationshipsSchema maintenanceFrameworkBioscience applicationsResearch focusQueriesMetadataDatabaseUMLSUsersData extractionDifferent subsetsSchemaParticular research focusTemporal query of attribute-value patient data: utilizing the constraints of clinical studies
Deshpande AM, Brandt C, Nadkarni PM. Temporal query of attribute-value patient data: utilizing the constraints of clinical studies. International Journal Of Medical Informatics 2003, 70: 59-77. PMID: 12706183, PMCID: PMC2987270, DOI: 10.1016/s1386-5056(02)00183-1.Peer-Reviewed Original ResearchConceptsClinical study data management systemsTemporal queriesClinical patient record systemsClinical data storageData management systemPatient record systemQuery algorithmData storageTemporal operatorsClinical studiesQueriesManagement systemGroup of patientsRecord systemEffect of therapyTemporal computationAdverse eventsRelational formsPatient dataLogistic reasonsArchitectureValue modelAlgorithmTrialDB: A web-based Clinical Study Data Management System.
Brandt CA, Deshpande AM, Lu C, Ananth G, Sun K, Gadagkar R, Morse R, Rodriguez C, Miller PL, Nadkarni PM. TrialDB: A web-based Clinical Study Data Management System. AMIA Annual Symposium Proceedings 2003, 2003: 794. PMID: 14728299, PMCID: PMC1480035.Peer-Reviewed Original ResearchConceptsClinical study data management systemsData management systemClass of softwareManagement systemPre-existing softwareWeb-based technologiesOpen source formDatabase engineClinical domainsSuch softwareData managementCentralized managementDifferent clinical domainsChallenging taskSuch systemsValue modelingSoftwareRequisite functionalityIntranetInternetDiverse typesSystemTaskDomainEngineIntegrating Query of Relational and Textual Data in Clinical Databases: A Case Study
Fisk JM, Mutalik P, Levin FW, Erdos J, Taylor C, Nadkarni P. Integrating Query of Relational and Textual Data in Clinical Databases: A Case Study. Journal Of The American Medical Informatics Association 2003, 10: 21-38. PMID: 12509355, PMCID: PMC150357, DOI: 10.1197/jamia.m1133.Peer-Reviewed Original ResearchConceptsRelational database management systemInformation retrievalDatabase management systemClinical data martCommodity softwareFuzzy searchingText indexingRelational searchTextual dataData martIR softwareBoolean searchManagement systemMedical textsSoftwareSearchingDocumentsQueriesTextIndexingClinical databaseCase studyIR facilitiesRetrievalVendors
2002
Metadata-driven creation of data marts from an EAV-modeled clinical research database
Brandt CA, Morse R, Matthews K, Sun K, Deshpande AM, Gadagkar R, Cohen DB, Miller PL, Nadkarni PM. Metadata-driven creation of data marts from an EAV-modeled clinical research database. International Journal Of Medical Informatics 2002, 65: 225-241. PMID: 12414020, DOI: 10.1016/s1386-5056(02)00047-3.Peer-Reviewed Original ResearchMeSH KeywordsBreast NeoplasmsDatabase Management SystemsDatabases as TopicFemaleHumansInformation Storage and RetrievalMedical Informatics ApplicationsSoftwareConceptsData martClinical study data management systemsTransaction-oriented systemsData management systemClinical research databaseDatabase schemaEntity attributesAnalytical processingHuman interpretationStudy metadataMetadataManagement systemArbitrary numberData entrySuch dataBrowsingValue modelSchemaMartHigher-level groupingsSystemDataProcessingDatabaseCreationMetadata-driven Ad Hoc Query of Patient Data
Deshpande AM, Brandt C, Nadkarni PM. Metadata-driven Ad Hoc Query of Patient Data. Journal Of The American Medical Informatics Association 2002, 9: 369-382. PMID: 12087118, PMCID: PMC346624, DOI: 10.1197/jamia.m1034.Peer-Reviewed Original ResearchConceptsClinical study data management systemsClinical patient record systemsQuery interfaceAd-Hoc QueriesData management systemWeb-based platformPatient record systemManagement systemClinical studiesRecord systemMetadataStandardized therapeutic interventionsUnderlying clinical conditionSystem operationNon-research settingsClinical parametersPatient managementClinical conditionsQueriesPortingTherapeutic interventionsInterfaceSystemPlatformAD
2001
Easing the transition between attribute-value databases and conventional databases for scientific data.
Nadkarni P, Marenco L. Easing the transition between attribute-value databases and conventional databases for scientific data. AMIA Annual Symposium Proceedings 2001, 483-7. PMID: 11825235, PMCID: PMC2243470.Peer-Reviewed Original ResearchMeSH KeywordsDatabase Management SystemsDatabases as TopicSystems IntegrationUser-Computer InterfaceConceptsEAV/CRData transfer toolsData transfer programProgrammer interventionConventional databasesLegacy systemsDB technologyDevelopment frameworkGeneric toolData sourcesDifferent representationsConventional dataAnalytical packageDatabaseScientific dataTransfer toolsScientific databasesTransfer taskToolProgrammingTaskCurrent limitationsWide varietyTechnologyFramework
2000
Reengineering a Database for Clinical Trials Management Lessons for System Architects
Brandt C, Nadkarni P, Marenco L, Karras B, Lu C, Schacter L, Fisk J, Miller P. Reengineering a Database for Clinical Trials Management Lessons for System Architects. Contemporary Clinical Trials 2000, 21: 440-461. PMID: 11018562, DOI: 10.1016/s0197-2456(00)00070-2.Peer-Reviewed Original ResearchExploring Performance Issues for a Clinical Database Organized Using an Entity-Attribute-Value Representation
Chen R, Nadkarni P, Marenco L, Levin F, Erdos J, Miller P. Exploring Performance Issues for a Clinical Database Organized Using an Entity-Attribute-Value Representation. Journal Of The American Medical Informatics Association 2000, 7: 475-487. PMID: 10984467, PMCID: PMC79043, DOI: 10.1136/jamia.2000.0070475.Peer-Reviewed Original ResearchMeSH KeywordsDatabase Management SystemsDatabases as TopicDatabases, FactualInformation Storage and RetrievalMicrobiologyPilot ProjectsConceptsEAV/CRDatabase schemaSQL statementsDatabase modelDatabase sizeSystem memoryQuery execution timeHeterogeneous biomedical dataSimple SQL statementsQuery efficiencyQuery performancePowerful hardwareQuery strategyEntity attributesDatabase queriesDatabase representationBiomedical dataExecution timeQueriesMore memoryPerformance issuesSchemaValue representationRepresentationCR modelIntegration of a hematopoietic progenitor cell program using the ACT/DB database system
Perrotta P, Nadkarni P. Integration of a hematopoietic progenitor cell program using the ACT/DB database system. Computer Methods And Programs In Biomedicine 2000, 61: 195-207. PMID: 10710182, DOI: 10.1016/s0169-2607(99)00038-3.Peer-Reviewed Original ResearchConceptsClient-server databaseComprehensive software systemSQL Server databaseDiverse data requirementsWeb-based technologiesData entry formsSoftware systemsServer databaseDatabase systemsInformation technologyMicrosoft AccessControl functionalityEntry formData requirementsTechnologyInternetDatabaseQuality assuranceOracleDeploymentSoftwareSystemFunctionalityRequirementsProcessing