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 ResearchMeSH KeywordsDatabase Management SystemsDatabases as TopicInternetProgramming LanguagesSemanticsSoftwareVocabulary, ControlledConceptsEAV/CRXML-based protocolHuman Brain ProjectDatabase supportData querySemantic descriptorsAutomatic generationNeuroscience databasesCR frameworkScientific domainsBrain ProjectInterclass relationshipsSchema maintenanceFrameworkBioscience applicationsResearch focusQueriesMetadataDatabaseUMLSUsersData extractionDifferent subsetsSchemaParticular research focus
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
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 observersWeb-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 accessEnvironmentLispMaintainabilityApplications
1997
Concept Locator: A Client-Server Application for Retrieval of UMLS Metathesaurus Concepts through Complex Boolean Query
Nadkarni P. Concept Locator: A Client-Server Application for Retrieval of UMLS Metathesaurus Concepts through Complex Boolean Query. Journal Of Biomedical Informatics 1997, 30: 323-336. PMID: 9339325, DOI: 10.1006/cbmr.1997.1433.Peer-Reviewed Original ResearchMeSH KeywordsDatabase Management SystemsInformation Storage and RetrievalProgramming LanguagesUnified Medical Language SystemVocabulary, ControlledConceptsClient-server applicationsQuery expressionsQuery optimizerRelational database serverPurpose of retrievalComplex Boolean queriesMore SQL statementsComplex Boolean expressionsUMLS Metathesaurus conceptsDatabase serverBoolean queriesSQL statementsWildcard patternsUMLS MetathesaurusMetathesaurus conceptsBoolean expressions
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 ResearchMeSH KeywordsAlgorithmsComputer Communication NetworksEvaluation Studies as TopicGenetic LinkageProgramming LanguagesSoftwareConceptsParallel 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 ResearchMeSH KeywordsAlgorithmsComputer SystemsDatabases, FactualEvaluation Studies as TopicProgramming LanguagesSequence AlignmentSoftwareSoftware DesignConceptsDatabase of sequencesBiological sequence comparisonParallel computationMachine-independent parallel programming languageParallel programming languageHypercube parallel computerProgramming languageSoftware platformParallel computersParallel machinesExpressive powerBiological sequencesParallelizationPlatform programComputationModest sacrificeBenchmark testsLogicDatabaseCase studyComputerPortabilityMachineLindaRelative advantages
1991
Parallelizing genetic linkage analysis: A case study for applying parallel computation in molecular biology
Miller P, Nadkarni P, Gelernter J, Carriero N, Pakstis A, Kidd K. Parallelizing genetic linkage analysis: A case study for applying parallel computation in molecular biology. Journal Of Biomedical Informatics 1991, 24: 234-248. PMID: 1868693, DOI: 10.1016/0010-4809(91)90046-y.Peer-Reviewed Original ResearchMeSH KeywordsChromosome MappingForecastingGenetic LinkageLod ScoreMolecular BiologyProgramming LanguagesSoftwareSoftware DesignConceptsParallel computersSequential programsMachine-independent parallel programming languageParallel programming languageDifferent parallel machinesLengthy computation timeParallel programsProgramming languageAvailable processorsDifferent processorsParallel computationParallel machinesSequential versionParallel versionComputational loadComputation timePerformance benchmarksComputerProcessorsCase studyDifferent piecesIterative programsLINKMAPComputationParallel formsParallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm
Miller P, Nadkarni P, Carriero N. Parallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm. Bioinformatics 1991, 7: 71-78. PMID: 2004277, DOI: 10.1093/bioinformatics/7.1.71.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAmino Acid SequenceComputer SystemsMathematical ComputingMolecular Sequence DataProgramming LanguagesSoftware DesignConceptsSequence comparison algorithmAmount of computationMachine-independent parallel programming languageComparison algorithmsDisk I/OParallel programming languageParallel program runsO bottleneck problemDifferent parallel machinesBiological sequence comparisonNumber of processorsTime-consuming computationProgramming languageParallelization strategyParallel computationParallel machinesProgram design strategiesProgram runBottleneck problemFASTA algorithmFASTAAlgorithmComputationBottleneckGeneral problem