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 ResearchConceptsClinical 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
2005
Automating identification of adverse events related to abnormal lab results using standard vocabularies.
Brandt CA, Lu CC, Nadkarni PM. Automating identification of adverse events related to abnormal lab results using standard vocabularies. AMIA Annual Symposium Proceedings 2005, 2005: 903. PMID: 16779190, PMCID: PMC1560626.Peer-Reviewed Original Research
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 ResearchMeSH KeywordsArtificial IntelligenceComputer SystemsDatabase Management SystemsDecision Support Systems, ClinicalPilot ProjectsSoftwareVocabulary, ControlledConceptsMetadata 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 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 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
2001
UMLS Concept Indexing for Production Databases
Nadkarni P, Chen R, Brandt C. UMLS Concept Indexing for Production Databases. Journal Of The American Medical Informatics Association 2001, 8: 80-91. PMID: 11141514, PMCID: PMC134593, DOI: 10.1136/jamia.2001.0080080.Peer-Reviewed Original ResearchAbstracting and IndexingAlgorithmsFeasibility StudiesUnified Medical Language SystemVocabulary, Controlled
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