2023
Blockchain-enabled immutable, distributed, and highly available clinical research activity logging system for federated COVID-19 data analysis from multiple institutions
Kuo T, Pham A, Edelson M, Kim J, Chan J, Gupta Y, Ohno-Machado L, Anderson D, Balacha C, Bath T, Baxter S, Becker-Pennrich A, Bell D, Bernstam E, Ngan C, Day M, Doctor J, DuVall S, El-Kareh R, Florian R, Follett R, Geisler B, Ghigi A, Gottlieb A, Hinske L, Hu Z, Ir D, Jiang X, Kim K, Kim J, Knight T, Koola J, Kuo T, Lee N, Mansmann U, Matheny M, Meeker D, Mou Z, Neumann L, Nguyen N, Nick A, Ohno-Machado L, Park E, Paul P, Pletcher M, Post K, Rieder C, Scherer C, Schilling L, Soares A, SooHoo S, Soysal E, Steven C, Tep B, Toy B, Wang B, Wu Z, Xu H, Yong C, Zheng K, Zhou Y, Zucker R. Blockchain-enabled immutable, distributed, and highly available clinical research activity logging system for federated COVID-19 data analysis from multiple institutions. Journal Of The American Medical Informatics Association 2023, 30: 1167-1178. PMID: 36916740, PMCID: PMC10198529, DOI: 10.1093/jamia/ocad049.Peer-Reviewed Original ResearchConceptsFederated data analysisUser activity logsSmart contract deploymentRun-time efficiencyData analysis systemData analysis activitiesActivity logsData discoveryQuerying timeBlockchain systemBlockchain technologyNetwork transactionsCOVID-19 data analysisMultiple institutionsLow deploymentBlockchainGitHub repositoryMultiple nodesLarge networksQueriesAnalysis activitiesHigh availabilityLanguage codeBaseline solutionData analysis
2021
Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track
Kuo T, Bath T, Ma S, Pattengale N, Yang M, Cao Y, Hudson C, Kim J, Post K, Xiong L, Ohno-Machado L. Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track. International Journal Of Medical Informatics 2021, 154: 104559. PMID: 34474309, PMCID: PMC9933142, DOI: 10.1016/j.ijmedinf.2021.104559.Peer-Reviewed Original ResearchConceptsSecure genome analysis competitionData retrieval queriesBlockchain-based methodData sharing methodReal-world problemsQuery indexType of sharingRetrieval queriesBlockchain technologyLedger technologySource codeBlockchain utilizationBlockchain strategyHealthcare applicationsInteraction recordsSharing methodTest datasetSharing recordsBiomedical research applicationsConsortium resourcesNew platformPatient recordsBlockchainQueriesTechnology
2017
Information retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge
Roberts K, Gururaj A, Chen X, Pournejati S, Hersh W, Demner-Fushman D, Ohno-Machado L, Cohen T, Xu H. Information retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge. Database 2017, 2017: bax068. DOI: 10.1093/database/bax068.Peer-Reviewed Original ResearchBiomedical datasetsRetrieval challengesInformation retrieval techniquesAdvanced query processingBiomedical data repositoriesAdvanced retrieval methodsQuery processingInformation retrievalTest queriesRetrieval systemRank frameworkRetrieval approachRetrieval techniquesData repositoryRetrieval methodTop precisionDatasetQueriesRepositoryChallengesRetrievalTaskLearningSystemCorpus
2015
A system to build distributed multivariate models and manage disparate data sharing policies: implementation in the scalable national network for effectiveness research
Meeker D, Jiang X, Matheny M, Farcas C, D’Arcy M, Pearlman L, Nookala L, Day M, Kim K, Kim H, Boxwala A, El-Kareh R, Kuo G, Resnic F, Kesselman C, Ohno-Machado L. A system to build distributed multivariate models and manage disparate data sharing policies: implementation in the scalable national network for effectiveness research. Journal Of The American Medical Informatics Association 2015, 22: 1187-1195. PMID: 26142423, PMCID: PMC4639714, DOI: 10.1093/jamia/ocv017.Peer-Reviewed Original ResearchConceptsFederated networkData sharing policiesParallel computation methodSharing policiesPolicy management systemData exchange policiesData storage requirementsWeb servicesNetwork queriesQuery functionalityComputation resourcesFederated modelGraphical interfaceData transportCentralized networkStorage requirementsNetwork participantsManagement systemQueriesNetworkComputation methodNew featuresMultivariate statistical estimationDifferent state lawsImportant new feature
2014
PhenDisco: phenotype discovery system for the database of genotypes and phenotypes
Doan S, Lin K, Conway M, Ohno-Machado L, Hsieh A, Feupe S, Garland A, Ross M, Jiang X, Farzaneh S, Walker R, Alipanah N, Zhang J, Xu H, Kim H. PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. Journal Of The American Medical Informatics Association 2014, 21: 31-36. PMID: 23989082, PMCID: PMC3912702, DOI: 10.1136/amiajnl-2013-001882.Peer-Reviewed Original ResearchConceptsNew information retrieval systemInformation retrieval systemsInformation retrieval toolsDatabase of GenotypesText processing toolsRetrieval systemSearch scenariosDiscovery systemRetrieval toolsAuthorized usersNon-standardized wayCross-study validationSearch comparisonProcessing toolsPromising performanceUsersPhenotype informationDatabaseInformationBiotechnology InformationQueriesMetadataEntrezResourcesSystem
2011
Quantifying fine-grained privacy risk and representativeness in medical data
Jiang X, Cheng S, Ohno-Machado L. Quantifying fine-grained privacy risk and representativeness in medical data. 2011, 64-67. DOI: 10.1145/2023582.2023594.Peer-Reviewed Original Research
2010
DSGeo: Software tools for cross-platform analysis of gene expression data in GEO
Lacson R, Pitzer E, Kim J, Galante P, Hinske C, Ohno-Machado L. DSGeo: Software tools for cross-platform analysis of gene expression data in GEO. Journal Of Biomedical Informatics 2010, 43: 709-715. PMID: 20435161, PMCID: PMC2934864, DOI: 10.1016/j.jbi.2010.04.007.Peer-Reviewed Original ResearchConceptsAggregation of dataData loaderRelational databaseGene expression dataUser preferencesData browserData browsingCross-platform dataSoftware toolsSeamless integrationCross-platform analysisGroups of dataQueriesExpression dataPublic gene expression dataSpecific sample characteristicsLarge resourcesBrowserToolBrowsingAnnotatingUsersRetrievalApplicationsPlatform
1997
A virtual repository approach to clinical and utilization studies: application in mammography as alternative to a national database.
Ohno-Machado L, Boxwala A, Ehresman J, Smith D, Greenes R. A virtual repository approach to clinical and utilization studies: application in mammography as alternative to a national database. AMIA Annual Symposium Proceedings 1997, 369-73. PMID: 9357650, PMCID: PMC2233552.Peer-Reviewed Original ResearchConceptsMammography databaseVisualization of resultsHeterogeneous databasesFederated databasesCentralized architectureExploratory analysis toolLegacy systemsCommon queriesPrototype systemQueriesVirtual repositoryAlternative architecturesImmediate displayDifferent databasesArchitectureAnalysis toolsMammography dataUse of dataRepositoryMammography reportsDatabaseUsersDownloadSystemVisualization