2025
A Novel Sentence Transformer-based Natural Language Processing Approach for Schema Mapping of Electronic Health Records to the OMOP Common Data Model.
Zhou X, Dhingra L, Aminorroaya A, Adejumo P, Khera R. A Novel Sentence Transformer-based Natural Language Processing Approach for Schema Mapping of Electronic Health Records to the OMOP Common Data Model. AMIA Annual Symposium Proceedings 2025, 2024: 1332-1339. PMID: 40417570.Peer-Reviewed Original ResearchConceptsCommon data modelElectronic health recordsOMOP Common Data ModelSchema mappingsMapping electronic health recordData modelTransformer-based deep learning modelsNatural language processing approachEnd-to-endDeep learning modelsHealth recordsEnhance interoperabilityTransformation pipelineLearning modelsOMOPProcessing approachSchemaStandard conceptsDiverse healthcare systemsInteroperabilityLarge-scaleStandard mapDatasetSoftwareHealthcare system
2023
Representing and utilizing clinical textual data for real world studies: An OHDSI approach
Keloth V, Banda J, Gurley M, Heider P, Kennedy G, Liu H, Liu F, Miller T, Natarajan K, V Patterson O, Peng Y, Raja K, Reeves R, Rouhizadeh M, Shi J, Wang X, Wang Y, Wei W, Williams A, Zhang R, Belenkaya R, Reich C, Blacketer C, Ryan P, Hripcsak G, Elhadad N, Xu H. Representing and utilizing clinical textual data for real world studies: An OHDSI approach. Journal Of Biomedical Informatics 2023, 142: 104343. PMID: 36935011, PMCID: PMC10428170, DOI: 10.1016/j.jbi.2023.104343.Peer-Reviewed Original ResearchConceptsNatural language processingCommon data modelTextual dataNLP solutionObservational Health Data SciencesOMOP Common Data ModelSpecific use casesObservational Medical Outcomes Partnership Common Data ModelHealth Data SciencesRepresentation of informationUse casesElectronic health recordsReal-world evidence generationData scienceClinical textData modelClinical notesLanguage processingHealth recordsLoad dataClinical documentationCurrent applicationsInformationWorkflowEvidence generationIntegrating real-world data to assess cardiac ablation device outcomes in a multicenter study using the OMOP common data model for regulatory decisions: implementation and evaluation
Yu Y, Jiang G, Brandt E, Forsyth T, Dhruva S, Zhang S, Chen J, Noseworthy P, Doshi A, Collison-Farr K, Kim D, Ross J, Coplan P, Drozda J. Integrating real-world data to assess cardiac ablation device outcomes in a multicenter study using the OMOP common data model for regulatory decisions: implementation and evaluation. JAMIA Open 2023, 6: ooac108. PMID: 36632328, PMCID: PMC9831049, DOI: 10.1093/jamiaopen/ooac108.Peer-Reviewed Original ResearchOMOP Common Data ModelCommon data modelData modelMedical device dataObservational Medical Outcomes Partnership Common Data ModelReal-world dataReal-world evaluationData integrationMultiple healthcare systemsData transformationHealthcare systemElectronic health record dataDevice dataData sourcesChain databaseLoad processHealth record dataTest casesMercy HealthQA analysisMulticenter studyMayo ClinicPatient outcomesPatient encountersDevice outcomes
2022
Extracting Patient-level Social Determinants of Health into the OMOP Common Data Model.
Phuong J, Zampino E, Dobbins N, Espinoza J, Meeker D, Spratt H, Madlock-Brown C, Weiskopf N, Wilcox A. Extracting Patient-level Social Determinants of Health into the OMOP Common Data Model. AMIA Annual Symposium Proceedings 2022, 2021: 989-998. PMID: 35308947, PMCID: PMC8861735.Peer-Reviewed Original Research
2021
A Comparison between Human and NLP-based Annotation of Clinical Trial Eligibility Criteria Text Using The OMOP Common Data Model.
Li X, Liu H, Kury F, Yuan C, Butler A, Sun Y, Ostropolets A, Xu H, Weng C. A Comparison between Human and NLP-based Annotation of Clinical Trial Eligibility Criteria Text Using The OMOP Common Data Model. AMIA Joint Summits On Translational Science Proceedings 2021, 2021: 394-403. PMID: 34457154, PMCID: PMC8378608.Peer-Reviewed Original ResearchCOVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model
Wang J, Abu-El-Rub N, Gray J, Pham H, Zhou Y, Manion F, Liu M, Song X, Xu H, Rouhizadeh M, Zhang Y. COVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model. Journal Of The American Medical Informatics Association 2021, 28: 1275-1283. PMID: 33674830, PMCID: PMC7989301, DOI: 10.1093/jamia/ocab015.Peer-Reviewed Original ResearchConceptsNatural language processing toolsCommon data modelLanguage processing toolsElectronic health recordsClinical natural language processing toolsData modelDeep learning-based modelProcessing toolsOMOP Common Data ModelPattern-based rulesObservational Medical Outcomes Partnership Common Data ModelLearning-based modelsSpecific information needsUse casesNLP toolsClinical textFree textExtensive evaluationDownloadable packageInformation needsHybrid approachResearch communityHealth recordsData sourcesHigh performance
2017
Feasibility of Representing Data from Published Nursing Research Using the OMOP Common Data Model.
Kim H, Choi J, Jang I, Quach J, Ohno-Machado L. Feasibility of Representing Data from Published Nursing Research Using the OMOP Common Data Model. AMIA Annual Symposium Proceedings 2017, 2016: 715-723. PMID: 28269868, PMCID: PMC5333244.Peer-Reviewed Original ResearchConceptsOMOP Common Data ModelNursing intervention protocolPatient reported outcomesCommon data modelReported outcomesDrug treatmentIntervention protocolUnique data itemsNursing articlesData modelNursing researchHealth dataPotential information lossData discoveryUse casesData itemsRepresenting DataFollowInformation lossDisease
2015
Creating a Common Data Model for Comparative Effectiveness with the Observational Medical Outcomes Partnership
FitzHenry F, Resnic F, Robbins S, Denton J, Nookala L, Meeker D, Ohno-Machado L, Matheny M. Creating a Common Data Model for Comparative Effectiveness with the Observational Medical Outcomes Partnership. Applied Clinical Informatics 2015, 06: 536-547. PMID: 26448797, PMCID: PMC4586341, DOI: 10.4338/aci-2014-12-cr-0121.Peer-Reviewed Original ResearchConceptsOMOP Common Data ModelPerson monthsHealth systemCount of medicationsMore outpatient visitsHealth system databaseMedication administration recordsComparative effectiveness analysisObservational Medical Outcomes Partnership (OMOP) CDMPharmacy fillsEligible cohortOutpatient visitsHigh prevalenceMedicationsComparative effectivenessAdministration recordsCommon data modelCohortMini-SentinelObservational Medical Outcomes PartnershipMonths
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