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 ResearchService-oriented Architecture in Medical Software: Promises and Perils
Nadkarni P, Miller R. Service-oriented Architecture in Medical Software: Promises and Perils. Journal Of The American Medical Informatics Association 2007, 14: 244-246. PMID: 17213485, PMCID: PMC2213462, DOI: 10.1197/jamia.m2349.Peer-Reviewed Original Research
2006
Pivoting approaches for bulk extraction of Entity–Attribute–Value data
Dinu V, Nadkarni P, Brandt C. Pivoting approaches for bulk extraction of Entity–Attribute–Value data. Computer Methods And Programs In Biomedicine 2006, 82: 38-43. PMID: 16556470, DOI: 10.1016/j.cmpb.2006.02.001.Peer-Reviewed Original ResearchConceptsEntity attributesClinical study data management systemsData management systemNumber of attributesDatabase serverHash tableClinical patient dataValue dataManagement systemAlternative algorithmsPatient dataSQLServerRepositoryAlgorithmComplex approachFormatDataAttributesParameter formatOne-columnExtractionAnalytical programPerformanceMemory
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 focusIntegrating 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 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
2001
Use of General-purpose Negation Detection to Augment Concept Indexing of Medical Documents
Mutalik P, Deshpande A, Nadkarni P. Use of General-purpose Negation Detection to Augment Concept Indexing of Medical Documents. Journal Of The American Medical Informatics Association 2001, 8: 598-609. PMID: 11687566, PMCID: PMC130070, DOI: 10.1136/jamia.2001.0080598.Peer-Reviewed Original ResearchConceptsNegation detectionMedical documentsUMLS conceptsProgramming language compilersFinite state machinesLanguage compilerConcept indexingMedical narrativesContext-free grammarsConcept matchingLexical scannerAbsence of negationDifferent test setsFormal languageState machinesRegular expressionsReliability of detectionDiverse training setConcept IDsTraining setParserHuman observationTest setLarge setHuman observers
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
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 optionsSpecification
1997
Mapdiff: determining differences between two genomic maps
Nadkarni P. Mapdiff: determining differences between two genomic maps. Bioinformatics 1997, 13: 217-225. PMID: 9183523, DOI: 10.1093/bioinformatics/13.3.217.Peer-Reviewed Original Research
1996
DNA Workbench: A Database Package to Manage Regional Physical Mapping
Nadkarni P, Cheung K, Castiglione C, Miller P, Kidd K. DNA Workbench: A Database Package to Manage Regional Physical Mapping. Journal Of Computational Biology 1996, 3: 319-329. PMID: 8811490, DOI: 10.1089/cmb.1996.3.319.Peer-Reviewed Original Research
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: 479-99. PMID: 8770535, DOI: 10.1016/s0010-4809(85)71030-0.Peer-Reviewed Original ResearchMeSH KeywordsComputer Communication NetworksComputer SecurityComputer SystemsEquipment FailureSoftwareConceptsDatabase application developmentStructured query languageApplication developmentCommon database operationsClient-server modeRapid application prototypingClient machineQuery languageDatabase operationsDatabase serverServer dataUser actionsApplication prototypingAccess rightsData dictionaryMicrocomputer databaseMetadataRelational formsClientsBiomedical databasesModest effortDictionaryServerFrameworkDatabase
1994
A modification of the ALIGN program to assist visual interpretation of mutated sequences
Nadkarni P, Reeders S, Zhou J. A modification of the ALIGN program to assist visual interpretation of mutated sequences. Bioinformatics 1994, 10: 361-362. PMID: 7922696, DOI: 10.1093/bioinformatics/10.3.361.Peer-Reviewed Original ResearchGDBDICT: A Program to Extract GDB Schema Information into a Relational Database
Nadkarni P. GDBDICT: A Program to Extract GDB Schema Information into a Relational Database. Genomics 1994, 19: 185-186. PMID: 8188228, DOI: 10.1006/geno.1994.1040.Peer-Reviewed Original Research
1992
Harnessing networked workstations as a powerful parallel computer: a general paradigm illustrated using three programs for genetic linkage analysis
Miller P, Nadkarni P, Bercovitz P. Harnessing networked workstations as a powerful parallel computer: a general paradigm illustrated using three programs for genetic linkage analysis. Bioinformatics 1992, 8: 141-147. PMID: 1591609, DOI: 10.1093/bioinformatics/8.2.141.Peer-Reviewed Original ResearchConceptsParallel computersMachine-independent parallel programming languageParallel programming languagePowerful parallel computersParallel programsProgramming languageNetworked workstationsComputational resourcesParallel machinesGeneral paradigmBiological computationWorkstationsComputerLindaNetworkInstitutions networkMathematical techniquesParadigmHardwareMachineComputationLanguageCapabilityResourcesComparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison
Miller P, Nadkarni P, Pearson W. Comparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison. Bioinformatics 1992, 8: 167-175. PMID: 1591612, DOI: 10.1093/bioinformatics/8.2.167.Peer-Reviewed Original ResearchConceptsDatabase of sequencesBiological sequence comparisonParallel computationMachine-independent parallel programming languageParallel programming languageHypercube parallel computerProgramming languageSoftware platformParallel computersParallel machinesExpressive powerBiological sequencesParallelizationPlatform programComputationModest sacrificeBenchmark testsLogicDatabaseCase studyComputerPortabilityMachineLindaRelative advantages