2016
Chapter 9 Clinical Data Repositories: Warehouses, Registries, and the Use of Standards
Nadkarni P. Chapter 9 Clinical Data Repositories: Warehouses, Registries, and the Use of Standards. 2016, 173-185. DOI: 10.1016/b978-0-12-803130-8.00009-9.Peer-Reviewed Original ResearchOperational data storeData martVirtual data integrationClinical data martClinical data warehouseData storesData warehouseData integrationRapid queryData repositoryData elementsUse of standardsWarehouseData sourcesRepositoryPhysical integrationProcess of extractionQueriesDifferent kindsMartUsabilityData extractionChapter 3 Core Informatics Technologies: Data Storage
Nadkarni P. Chapter 3 Core Informatics Technologies: Data Storage. 2016, 49-84. DOI: 10.1016/b978-0-12-803130-8.00003-8.Peer-Reviewed Original ResearchInformation retrievalData elementsText information retrievalInformatics/computer scienceRetrieval of dataIndexing technologyUnstructured textRelational databaseDatabase indexResearch computingComputer scienceData storageRetrievalLarge volumesEfficient operationTechnologyNoSQLComputingQueriesBrief introductionCritical componentStorageProcessingTechnological armamentariumDatabase
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
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
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 expertise
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 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 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
2000
Exploring 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 ResearchConceptsEAV/CRDatabase schemaSQL statementsDatabase modelDatabase sizeSystem memoryQuery execution timeHeterogeneous biomedical dataSimple SQL statementsQuery efficiencyQuery performancePowerful hardwareQuery strategyEntity attributesDatabase queriesDatabase representationBiomedical dataExecution timeQueriesMore memoryPerformance issuesSchemaValue representationRepresentationCR model
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
Management of Evolving Map Data: Data Structures and Algorithms Based on the Framework Map
Nadkarni P. Management of Evolving Map Data: Data Structures and Algorithms Based on the Framework Map. Genomics 1995, 30: 565-573. PMID: 8825644, DOI: 10.1006/geno.1995.1278.Peer-Reviewed Original ResearchConceptsData structureMap maintenanceClient-server databaseRelational databaseAmount of informationGenomic objectsAlgorithm BasedMap dataAlgorithmConsensus framework mapUseful mapsGenome CenterDatabaseObjectsQueriesMapsPutative orderBasedMapping effortsInformationFramework mapDataApplicationsOrderHeterogeneous methodologies