2013
Natural language processing: algorithms and tools to extract computable information from EHRs and from the biomedical literature
Ohno-Machado L, Nadkarni P, Johnson K. Natural language processing: algorithms and tools to extract computable information from EHRs and from the biomedical literature. Journal Of The American Medical Informatics Association 2013, 20: 805-805. PMID: 23935077, PMCID: PMC3756279, DOI: 10.1136/amiajnl-2013-002214.Commentaries, Editorials and LettersMeSH KeywordsAlgorithmsDatabases, BibliographicElectronic Health RecordsInformation Storage and RetrievalNatural Language Processing
2011
Data standards for clinical research data collection forms: current status and challenges
Richesson R, Nadkarni P. Data standards for clinical research data collection forms: current status and challenges. Journal Of The American Medical Informatics Association 2011, 18: 341-346. PMID: 21486890, PMCID: PMC3078665, DOI: 10.1136/amiajnl-2011-000107.Peer-Reviewed Original ResearchMeSH KeywordsBiomedical ResearchData CollectionForms and Records ControlHumansInformation Storage and RetrievalReference StandardsSurveys and QuestionnairesUser-Computer InterfaceVocabulary, ControlledConceptsClinical Research InformaticsStandards adoptionWorkflow supportStructured data collectionData itemsResearch informaticsData standardsTool requirementsStandards effortsSuch toolsTerminological standardsResearch data collectionClinical research applicationsContent standardsData collectionInteroperabilityCase report formsResearch applicationsAdoptionInformaticsResearch activitiesRetrievalToolFormal relationshipReuse
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
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 ResearchMeSH KeywordsDatabases, FactualHumansInformation DisseminationInformation Storage and RetrievalInternetNeurosciencesSoftwareSystems IntegrationInteroperability 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 dataAlgorithmSoftwareToolFormatDataHongyuInterfaceIntegrationPackageApplicationsQIS: 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 expertiseIntegration of Web-based and PC-based Clinical Research Databases
Brandt CA, Sun K, Charpentier P, Nadkarni PM. Integration of Web-based and PC-based Clinical Research Databases. Methods Of Information In Medicine 2004, 43: 287-295. PMID: 15227559, DOI: 10.1055/s-0038-1633870.Peer-Reviewed Original ResearchMeSH KeywordsAgedBiomedical ResearchDatabase Management SystemsGeriatricsHumansInformation Storage and RetrievalInternetMicrocomputersSystems IntegrationUnified Medical Language SystemUnited StatesUser-Computer InterfaceConceptsDatabase applicationsClinical study data management systemsIntegration of applicationsCommon semantic modelData management systemWeb-based repositoryClinical research databaseSchema conflictsSharing of featuresData managementMapping schemaSemantic modelDifferent operating environmentsModel unificationManagement systemIntegration effortsOperating environmentArea of applicabilityData collectionMajor benefitsSimilar purposesIntegrationApplicationsCritical conflictsData libraries
2003
Text mining neuroscience journal articles to populate neuroscience databases
Crasto CJ, Marenco LN, Migliore M, Mao B, Nadkarni PM, Miller P, Shepherd GM. Text mining neuroscience journal articles to populate neuroscience databases. Neuroinformatics 2003, 1: 215-237. PMID: 15046245, DOI: 10.1385/ni:1:3:215.Peer-Reviewed Original ResearchConceptsNeuroscience databasesNatural language textPre-processing stepDatabase architectureLanguage textRetrieval resultsDatabase keywordsSemantic contextBibliography databasesNeuroscience articlesTest setTwo-step approachFirst stepDatabaseExpertsArchitectureSoftwareKnowledgebaseSecond stepNeuroscienceSenseLabKeywordsContinual improvementStepAccuracyCreating knowledgebases to text-mine PUBMED articles using clustering techniques.
Crasto CJ, Morse TM, Migliore M, Nadkarni P, Hines M, Brash DE, Miller PL, Shepherd GM. Creating knowledgebases to text-mine PUBMED articles using clustering techniques. AMIA Annual Symposium Proceedings 2003, 2003: 821. PMID: 14728326, PMCID: PMC1479923.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsArtificial IntelligenceDatabases as TopicHumansInformation Storage and RetrievalNeurologyPubMedIntegrating 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 ResearchMeSH KeywordsBreast NeoplasmsDatabase Management SystemsDatabases as TopicFemaleHumansInformation Storage and RetrievalMedical Informatics ApplicationsSoftwareConceptsData 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 ResearchMeSH KeywordsComputer SecurityDatabase Management SystemsHumansInformation Storage and RetrievalInternetMedical Records Systems, ComputerizedProgramming LanguagesResearchSoftwareUser-Computer InterfaceConceptsClinical 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 ResearchMeSH KeywordsAbstracting and IndexingInformation Storage and RetrievalMedical RecordsNatural Language ProcessingProgramming LanguagesSoftwareUnified Medical Language SystemConceptsNegation 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 observersIntegration 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 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
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 modelExploring the Degree of Concordance of Coded and Textual Data in Answering Clinical Queries from a Clinical Data Repository
Stein H, Nadkarni P, Erdos J, Miller P. Exploring the Degree of Concordance of Coded and Textual Data in Answering Clinical Queries from a Clinical Data Repository. Journal Of The American Medical Informatics Association 2000, 7: 42-54. PMID: 10641962, PMCID: PMC61454, DOI: 10.1136/jamia.2000.0070042.Peer-Reviewed Original ResearchHernia, VentralHumansInformation Storage and RetrievalMedical Records Systems, ComputerizedPostoperative ComplicationsPulmonary EmbolismSurgical Wound Infection
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 ResearchMeSH KeywordsAnimalsChromosome MappingDatabases, FactualEukaryotic CellsGene ExpressionInformation Storage and RetrievalInternetModels, MolecularMultigene FamilyReceptors, OdorantSequence HomologyUser-Computer InterfaceNeuronal 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