2016
Quality of EHR data extractions for studies of preterm birth in a tertiary care center: guidelines for obtaining reliable data
Knake L, Ahuja M, McDonald E, Ryckman K, Weathers N, Burstain T, Dagle J, Murray J, Nadkarni P. Quality of EHR data extractions for studies of preterm birth in a tertiary care center: guidelines for obtaining reliable data. BMC Pediatrics 2016, 16: 59. PMID: 27130217, PMCID: PMC4851819, DOI: 10.1186/s12887-016-0592-z.Peer-Reviewed Original ResearchConceptsEHR data extractionElectronic health recordsWhite blood cell countTertiary care centerData extractionBlood cell countInitial hemoglobinNeonatal recordsChart reviewFuture study designsPreterm birthChart extractionGestational ageOutside hospitalManual data abstractionBirth weightCare centerDirect bilirubinLaboratory valuesCell countBirth dataStudy designHealth recordsManual abstractionGuidelines
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 practice
2007
SenseLab: new developments in disseminating neuroscience information
Crasto CJ, Marenco LN, Liu N, Morse TM, Cheung KH, Lai PC, Bahl G, Masiar P, Lam HY, Lim E, Chen H, Nadkarni P, Migliore M, Miller PL, Shepherd GM. SenseLab: new developments in disseminating neuroscience information. Briefings In Bioinformatics 2007, 8: 150-162. PMID: 17510162, PMCID: PMC2756159, DOI: 10.1093/bib/bbm018.Peer-Reviewed Original ResearchInteroperability 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
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 dataAlgorithmSoftwareToolFormatDataHongyuInterfaceIntegrationPackageApplications
2003
Integrating 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
2001
Integration of Multidisciplinary Sensory Data
Miller P, Nadkarni P, Singer M, Marenco L, Hines M, Shepherd G. Integration of Multidisciplinary Sensory Data. Journal Of The American Medical Informatics Association 2001, 8: 34-48. PMID: 11141511, PMCID: PMC134590, DOI: 10.1136/jamia.2001.0080034.Peer-Reviewed Original ResearchConceptsNeuroinformatics researchFlexible data modelDiverse heterogeneous dataHuman Brain ProjectNew informatics technologiesHeterogeneous dataData modelSensory dataRelated toolsInformatics technologiesBrain ProjectBuilding databaseSingle unifying frameworkUnifying frameworkProject approachIntegrationComputer modelWeb-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 ResearchConceptsWeb 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 accessEnvironmentLispMaintainabilityApplications
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 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 assuranceOracleDeploymentSoftwareSystemFunctionalityRequirementsProcessingOlfactory 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 ResearchNeuronal 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 ResearchMeSH KeywordsDatabases, FactualHumansHypermediaInformation Storage and RetrievalInternetNervous SystemSystems Integration
1998
Database tools for integrating and searching membrane property data correlated with neuronal morphology
Mirsky J, Nadkarni P, Healy M, Miller P, Shepherd G. Database tools for integrating and searching membrane property data correlated with neuronal morphology. Journal Of Neuroscience Methods 1998, 82: 105-121. PMID: 10223520, DOI: 10.1016/s0165-0270(98)00049-1.Peer-Reviewed Original ResearchConceptsDatabase toolsWeb resourcesSearch toolsCritical problemUsersSequence databasesSimple canonical modelFunctional operationDatabaseToolSearchDifferent neuronsInternetAnnotationEquivalent compartmentsModelersDataProperty dataCanonical modelDifferent typesInformationState of acceptanceResourcesVehiclesProperty spaceA 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 ResearchMeSH KeywordsChromosome MappingComputational BiologyComputer SimulationDatabase Management SystemsDatabases, FactualMolecular BiologyConceptsMolecular 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 ResearchMeSH KeywordsAlgorithmsDatabases as TopicDatabases, FactualGenome, HumanHuman Genome ProjectHumansInformation Storage and RetrievalMethodsPilot Projects
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 formRepresentationOlfactory Receptor Database (ORDB): A Resource for Sharing and Analyzing Published and Unpublished Data
Healy M, Smith J, Singer M, Nadkarni P, Skoufos E, Miller P, Shepherd G. Olfactory Receptor Database (ORDB): A Resource for Sharing and Analyzing Published and Unpublished Data. Chemical Senses 1997, 22: 321-326. PMID: 9218144, DOI: 10.1093/chemse/22.3.321.Peer-Reviewed Original Research
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 issuesTechnologyCONTIG EXPLORER: Interactive Marker-Content Map Assembly
Nadkarni P, Banks A, Montgomery K, LeBlanc-Stracewski J, Miller P, Krauter K. CONTIG EXPLORER: Interactive Marker-Content Map Assembly. Genomics 1996, 31: 301-310. PMID: 8838311, DOI: 10.1006/geno.1996.0052.Peer-Reviewed Original Research