2014
Chapter 2 Data Integration: An Overview
Nadkarni P, Marenco L. Chapter 2 Data Integration: An Overview. 2014, 15-47. DOI: 10.1016/b978-0-12-401678-1.00002-6.Peer-Reviewed Original ResearchIntegration effortsIntermediary softwareSeamless accessData integration strategyPhysical integrationVirtual integrationData integrationTypes of dataData elementsLogical integrationSource systemSingle large organizationLarge organizationsSingle resourceUsersMultiple sourcesIntegration strategyIntegrationFormal sequenceQueriesMetadataSoftwareStorage technologiesRedundancySystem
2011
Metadata-driven Software Systems in Biomedicine, Designing Systems that can adapt to Changing Knowledge
Nadkarni P. Metadata-driven Software Systems in Biomedicine, Designing Systems that can adapt to Changing Knowledge. Health Informatics 2011 DOI: 10.1007/978-0-85729-510-1.Peer-Reviewed Original ResearchSoftware systemsClinical study data management systemsBiomedical database systemsData management systemResearch support systemSoftware developmentDatabase schemaDatabase systemsExtensible designSoftware historyDesigning systemSupport systemManagement systemSuch systemsDevelopment skillsElectronic medical recordsNon-trivial examplesNew systemProblems oneBest systemDetailed projectMetadataOntologyCase studySystem
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
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 Research
2005
Metadata-driven Delphi rating on the Internet
Deshpande AM, Shiffman RN, Nadkarni PM. Metadata-driven Delphi rating on the Internet. Computer Methods And Programs In Biomedicine 2005, 77: 49-56. PMID: 15639709, DOI: 10.1016/j.cmpb.2004.05.006.Peer-Reviewed Original ResearchConceptsDelphi ratingPaper-based data collectionTraditional paper-based methodsReusable softwarePaper-based methodsProgramming codeData entrySoftwareAnalysis toolsMetadataComputerized techniqueData collectionValues schemaInternetSchemaFive-level Likert scaleWebCodeDisagreement indexGuideline StandardizationExpertsToolMethodCostCollection
2004
QIS: 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 ResearchConceptsMetadata managementClinical study data management systemsHigh-level specificationData management systemProduction rule systemMiddleware enginesUse casesMetadata modificationCentralized informationStudy metadataManagement systemMetadataInformationSubschemaSystemSoftwareSpecificationEngineCapabilitySpecific typesManagement
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 ResearchConceptsEAV/CRXML-based protocolHuman Brain ProjectDatabase supportData querySemantic descriptorsAutomatic generationNeuroscience databasesCR frameworkScientific domainsBrain ProjectInterclass relationshipsSchema maintenanceFrameworkBioscience applicationsResearch focusQueriesMetadataDatabaseUMLSUsersData extractionDifferent subsetsSchemaParticular research focus
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 ResearchConceptsData 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
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 examplesArchitectureTaskFeaturesFrameworkVehicles
1999
Neuronal database integration: the Senselab EAV data model.
Marenco L, Nadkarni P, Skoufos E, Shepherd G, Miller P. Neuronal database integration: the Senselab EAV data model. AMIA Annual Symposium Proceedings 1999, 102-6. PMID: 10566329, PMCID: PMC2232788.Peer-Reviewed Original Research
1998
Data 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 ResearchConceptsElectronic patient record systemQuery problemAd-Hoc QueriesReal-time retrievalPatient record systemData warehousingEntity attributesComplex subproblemsData retrievalQueriesValue databaseRecord systemSuch systemsRetrievalValue tablePatient dataFront endAttributesMetadataWarehousingDatabaseUsersData extractionSubproblemsIndividual attributesA metadata approach to query interoperation between molecular biology databases.
Cheung KH, Nadkarni PM, Shin DG. A metadata approach to query interoperation between molecular biology databases. Bioinformatics 1998, 14: 486-497. PMID: 9694987, DOI: 10.1093/bioinformatics/14.6.486.Peer-Reviewed Original ResearchConceptsMolecular biology databasesDatabase objectsBiology databasesSpecification of correspondencesDatabase accessHeterogeneous databasesSQL queriesDatabase interoperationMetadata approachSuch metadataPrototype systemIndividual databasesInteroperationMap databaseMetadataDatabaseGreat challengeObjectsQueriesUsersValue modelDatabase comparisonRequestsSpecificationComplexityAutomatic query mapping among genomic databases: a pilot exploration.
Cheung KH, Nadkarni P, Miller P, Shin DG. Automatic query mapping among genomic databases: a pilot exploration. AMIA Annual Symposium Proceedings 1998, 942-6. PMID: 9929357, PMCID: PMC2232293.Peer-Reviewed Original Research
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 ResearchConceptsData retrievalClient-server applicationsGraphical front endSet-based queriesMetadata repositorySQL statementsData organizationKnowledge representationBiomedical databasesRetrievalProduction applicationsFront endQueriesServerMetadataDatabaseUsersRepositoryDatasetApplicationsRelation formRepresentation
1995
SQLGEN: A framework for rapid client-server database application development
Nadkarni P, Cheung K. SQLGEN: A framework for rapid client-server database application development. Journal Of Biomedical Informatics 1995, 28: 479-499. DOI: 10.1006/cbmr.1995.1030.Peer-Reviewed Original ResearchDatabase application developmentStructured query languageApplication developmentCommon database operationsClient-server modeRapid application prototypingClient machineQuery languageDatabase operationsDatabase serverServer dataUser actionsApplication prototypingAccess rightsData dictionaryMicrocomputer databaseMetadataRelational formsClientsBiomedical databasesModest effortDictionaryServerFrameworkDatabaseSQLGEN: a framework for rapid client-server database application development.
Nadkarni P, Cheung K. SQLGEN: a framework for rapid client-server database application development. Journal Of Biomedical Informatics 1995, 28: 479-99. PMID: 8770535, DOI: 10.1016/s0010-4809(85)71030-0.Peer-Reviewed Original ResearchConceptsDatabase application developmentStructured query languageApplication developmentCommon database operationsClient-server modeRapid application prototypingClient machineQuery languageDatabase operationsDatabase serverServer dataUser actionsApplication prototypingAccess rightsData dictionaryMicrocomputer databaseMetadataRelational formsClientsBiomedical databasesModest effortDictionaryServerFrameworkDatabase