2011
Web-browser encryption of personal health information
Morse R, Nadkarni P, Schoenfeld D, Finkelstein D. Web-browser encryption of personal health information. BMC Medical Informatics And Decision Making 2011, 11: 70. PMID: 22073940, PMCID: PMC3276430, DOI: 10.1186/1472-6947-11-70.Peer-Reviewed Original ResearchConceptsPersonal health informationRemote data entryWeb browserSensitive informationData centersHealth informationData entryHealth recordsUnprecedented amountPatient dataPatient confidentialityFinancial lossesClinical dataInformationMedical conditionsEncryptionServerBrowserClinical researchEffective medical practiceRange of situationsConfidentialityAccessSystemMedical practiceData standards for clinical research data collection forms: current status and challenges
Richesson R, Nadkarni P. Data standards for clinical research data collection forms: current status and challenges. Journal Of The American Medical Informatics Association 2011, 18: 341-346. PMID: 21486890, PMCID: PMC3078665, DOI: 10.1136/amiajnl-2011-000107.Peer-Reviewed Original ResearchConceptsClinical Research InformaticsStandards adoptionWorkflow supportStructured data collectionData itemsResearch informaticsData standardsTool requirementsStandards effortsSuch toolsTerminological standardsResearch data collectionClinical research applicationsContent standardsData collectionInteroperabilityCase report formsResearch applicationsAdoptionInformaticsResearch activitiesRetrievalToolFormal relationshipReuse
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
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 expertiseIntegration 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
Temporal 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 modelAlgorithmIntegrating 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 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
Web-based UMLS concept retrieval by automatic text scanning: a comparison of two methods
Brandt C, Nadkarni P. Web-based UMLS concept retrieval by automatic text scanning: a comparison of two methods. Computer Methods And Programs In Biomedicine 2001, 64: 37-43. PMID: 11084231, DOI: 10.1016/s0169-2607(00)00092-4.Peer-Reviewed Original ResearchMeSH KeywordsArtificial IntelligenceDatabases, FactualInformation Storage and RetrievalInternetProgramming LanguagesUnified Medical Language SystemUser-Computer InterfaceConceptsWeb applicationActive server pages (ASP) technologyAppropriate programming environmentApplication deliveryDatabase engineCode portabilityScripting environmentRelational databaseWeb developmentDevelopment environmentProgramming environmentConcept retrievalText scanningPage technologySuch functionalityRobust languageVendor implementationsRapid prototypingIdentical applicationsMedium of choiceEasy accessEnvironmentLispMaintainabilityApplicationsEasing 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
WebEAV
Nadkarni P, Brandt C, Marenco L. WebEAV. Journal Of The American Medical Informatics Association 2000, 7: 343-356. PMID: 10887163, PMCID: PMC61439, DOI: 10.1136/jamia.2000.0070343.Peer-Reviewed Original ResearchConceptsWeb development environmentWeb application developmentUser interface issuesClient-server technologyValue databaseWeb technologiesApplication developmentEntity attributesWeb developmentDevelopment environmentWeb interfaceGeneric frameworkInterface issuesComplex systemsFront endDatabaseTechnologyMetadataDevelopersSuitable examplesArchitectureTaskFeaturesFrameworkVehiclesOlfactory Receptor Database: a sensory chemoreceptor resource
Skoufos E, Marenco L, Nadkarni P, Miller P, Shepherd G. Olfactory Receptor Database: a sensory chemoreceptor resource. Nucleic Acids Research 2000, 28: 341-343. PMID: 10592268, PMCID: PMC102443, DOI: 10.1093/nar/28.1.341.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceChemoreceptor CellsDatabases, FactualMolecular Sequence DataOlfactory MucosaUser-Computer Interface
1999
Olfactory Receptor Database: a database of the largest eukaryotic gene family
Skoufos E, Healy M, Singer M, Nadkarni P, Miller P, Shepherd G. Olfactory Receptor Database: a database of the largest eukaryotic gene family. Nucleic Acids Research 1999, 27: 343-345. PMID: 9847223, PMCID: PMC148178, DOI: 10.1093/nar/27.1.343.Peer-Reviewed Original Research
1998
CHRONOMERGE: An Application for the Merging and Display of Multiple Time-Stamped Data Streams
Nadkarni P. CHRONOMERGE: An Application for the Merging and Display of Multiple Time-Stamped Data Streams. Journal Of Biomedical Informatics 1998, 31: 451-464. PMID: 9843629, DOI: 10.1006/cbmr.1998.1492.Peer-Reviewed Original ResearchConceptsData streamsGraphical user interfaceTime-stamped dataSingle streamTime-stamp valuesDatabase applicationsUser interfaceSQL codeMultiple time seriesMultiple streamsMerge operationResultant streamStatistical aggregatesStandard toolStreamsMore parametersMergeMultiple timesGranularityRepositoryTime seriesDisplayApplicationsNumerous optionsSpecificationData Extraction and Ad Hoc Query of an Entity—Attribute—Value Database
Nadkarni P, Brandt C. Data Extraction and Ad Hoc Query of an Entity—Attribute—Value Database. Journal Of The American Medical Informatics Association 1998, 5: 511-527. PMID: 9824799, PMCID: PMC61332, DOI: 10.1136/jamia.1998.0050511.Peer-Reviewed Original ResearchMeSH KeywordsClinical Trials as TopicDatabase Management SystemsHumansInformation Storage and RetrievalMedical Records Systems, ComputerizedUser-Computer InterfaceConceptsElectronic patient record systemQuery problemAd-Hoc QueriesReal-time retrievalPatient record systemData warehousingEntity attributesComplex subproblemsData retrievalQueriesValue databaseRecord systemSuch systemsRetrievalValue tablePatient dataFront endAttributesMetadataWarehousingDatabaseUsersData extractionSubproblemsIndividual attributesManaging Attribute–Value Clinical Trials Data Using the ACT/DB Client–Server Database System
Nadkarni P, Brandt C, Frawley S, Sayward F, Einbinder R, Zelterman D, Schacter L, Miller P. Managing Attribute–Value Clinical Trials Data Using the ACT/DB Client–Server Database System. Journal Of The American Medical Informatics Association 1998, 5: 139-151. PMID: 9524347, PMCID: PMC61285, DOI: 10.1136/jamia.1998.0050139.Peer-Reviewed Original ResearchMeSH KeywordsClinical Trials as TopicDatabase Management SystemsHumansMedical Records Systems, ComputerizedSoftware DesignUser-Computer InterfaceConceptsClient-server database systemsReuse of parametersData entryOracle serverDatabase applicationsDatabase systemsObject dataUNIX platformsDictionary searchData typesInitial deploymentLogical groupingPurposes of displaySuch dataStandard reportPilot useServerIndexingAnalysis programMachineDeploymentPlatformReuseClients
1997
QAV: querying entity-attribute-value metadata in a biomedical database
Nadkarni P. QAV: querying entity-attribute-value metadata in a biomedical database. Computer Methods And Programs In Biomedicine 1997, 53: 93-103. PMID: 9186046, DOI: 10.1016/s0169-2607(97)01815-4.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsDatabases, FactualHumansInformation Storage and RetrievalUser-Computer InterfaceConceptsData retrievalClient-server applicationsGraphical front endSet-based queriesMetadata repositorySQL statementsData organizationKnowledge representationBiomedical databasesRetrievalProduction applicationsFront endQueriesServerMetadataDatabaseUsersRepositoryDatasetApplicationsRelation formRepresentation
1996
ModelDB: An Environment for Running and Storing Computational Models and Their Results Applied to Neuroscience
Peterson B, Healy M, Nadkarni P, Miller P, Shepherd G. ModelDB: An Environment for Running and Storing Computational Models and Their Results Applied to Neuroscience. Journal Of The American Medical Informatics Association 1996, 3: 389-398. PMID: 8930855, PMCID: PMC116323, DOI: 10.1136/jamia.1996.97084512.Peer-Reviewed Original ResearchConceptsWorld Wide Web interfaceCluster of databasesHuman Brain ProjectWeb interfaceComputational modelIndividual databasesSmall databaseDatabase developmentBrain ProjectComplex informationRelated databasesFormal mannerVast quantitiesSystem functionDiverse sourcesDatabaseInformationWebProjectResearch groupsInitial approachPilot projectIssuesGeneral issuesTechnologyPhenoDB: An Integrated Client/Server Database for Linkage and Population Genetics
Cheung K, Nadkarni P, Silverstein S, Kidd J, Pakstis A, Miller P, Kidd K. PhenoDB: An Integrated Client/Server Database for Linkage and Population Genetics. Journal Of Biomedical Informatics 1996, 29: 327-337. PMID: 8812078, DOI: 10.1006/cbmr.1996.0024.Peer-Reviewed Original ResearchMeSH KeywordsAllelesComputer Communication NetworksComputer GraphicsComputer SystemsData Interpretation, StatisticalDatabase Management SystemsGene FrequencyGenetic LinkageGenetic MarkersGenetics, PopulationHumansInformation Storage and RetrievalInformation SystemsPedigreePhenotypeUser-Computer InterfaceConceptsClient/server databaseClient/server architectureData management tasksData analysis tasksUse graphical interfaceServer architectureDatabase applicationsComplex adServer databaseInteractive validationAnalysis tasksGraphical interfaceFile formatManagement tasksLarge datasetsPhenoDBMultipoint linkageGeneric formatHardy-Weinberg ratiosData entryEfficient managementProject managementGenetic marker dataPopulation geneticsTask