OBJECTIVE: Norwegian health registries covering entire population are used for administration, research, and emergency preparedness. We harmonized these data onto the Observational Medical Outcomes Partnership common data model (OMOP CDM) and enrich real-world data in OMOP format with COVID-19 related data.
METHODS: Data from six registries (2018-2021) covering birth registrations, selected primary and secondary care events, vaccinations, and communicable disease notifications were mapped onto the OMOP CDM v5.3. An Extract-Transform-Load (ETL) pipeline was developed on simulated data using data characterization documents and scanning tools. We ran dashboard quality checks, cohort generations, investigated differences between source and mapped data, and refined the ETL accordingly.
RESULTS: We mapped 1.5 billion rows of data of 5,673,845 individuals. Among these, there were 804,277 pregnancies, 483,585 mothers together with 792,477 children, and 472,948 fathers. We identified 382,516 positive tests for COVID-19 in 380,794 patients. These figures are consistent with results from source data. In addition to 11 million source codes mapped automatically, we mapped 237 non-standard codes to standard concepts and introduced 38 custom concepts to accommodate pregnancy-related terminologies that were not supported by OMOP CDM vocabularies. A total of 3,700/3,705 (99.8%) checks passed. The 5 failed checks could be explained by the nature of the data and only represent a small number of records.
CONCLUSIONS: Norwegian registry data were successfully harmonized onto OMOP CDM with high level of concordance and provides valuable source for federated COVID-19 related research. Our mapping experience is highly valuable for data partners with Nordic health registries.

BACKGROUND: Given the geographical sparsity of Rare Diseases (RDs), assembling a cohort is often a challenging task. Common data models (CDM) can harmonize disparate sources of data that can be the basis of decision support systems and artificial intelligence-based studies, leading to new insights in the field. This work is sought to support the design of large-scale multi-center studies for rare diseases.
METHODS: In an interdisciplinary group, we derived a list of elements of RDs in three medical domains (endocrinology, gastroenterology, and pneumonology) according to specialist knowledge and clinical guidelines in an iterative process. We then defined a RDs data structure that matched all our data elements and built Extract, Transform, Load (ETL) processes to transfer the structure to a joint CDM. To ensure interoperability of our developed CDM and its subsequent usage for further RDs domains, we ultimately mapped it to Observational Medical Outcomes Partnership (OMOP) CDM. We then included a fourth domain, hematology, as a proof-of-concept and mapped an acute myeloid leukemia (AML) dataset to the developed CDM.
RESULTS: We have developed an OMOP-based rare diseases common data model (RD-CDM) using data elements from the three domains (endocrinology, gastroenterology, and pneumonology) and tested the CDM using data from the hematology domain. The total study cohort included 61,697 patients. After aligning our modules with those of Medical Informatics Initiative (MII) Core Dataset (CDS) modules, we leveraged its ETL process. This facilitated the seamless transfer of demographic information, diagnoses, procedures, laboratory results, and medication modules from our RD-CDM to the OMOP. For the phenotypes and genotypes, we developed a second ETL process. We finally derived lessons learned for customizing our RD-CDM for different RDs.
CONCLUSIONS: This work can serve as a blueprint for other domains as its modularized structure could be extended towards novel data types. An interdisciplinary group of stakeholders that are actively supporting the project\'s progress is necessary to reach a comprehensive CDM.
CONCLUSIONS: The customized data structure related to our RD-CDM can be used to perform multi-center studies to test data-driven hypotheses on a larger scale and take advantage of the analytical tools offered by the OHDSI community.

UNASSIGNED: Patient-monitoring software generates a large amount of data that can be reused for clinical audits and scientific research. The Observational Health Data Sciences and Informatics (OHDSI) consortium developed the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) to standardize electronic health record data and promote large-scale observational and longitudinal research.
UNASSIGNED: This study aimed to transform primary care data into the OMOP CDM format.
UNASSIGNED: We extracted primary care data from electronic health records at a multidisciplinary health center in Wattrelos, France. We performed structural mapping between the design of our local primary care database and the OMOP CDM tables and fields. Local French vocabularies concepts were mapped to OHDSI standard vocabularies. To validate the implementation of primary care data into the OMOP CDM format, we applied a set of queries. A practical application was achieved through the development of a dashboard.
UNASSIGNED: Data from 18,395 patients were implemented into the OMOP CDM, corresponding to 592,226 consultations over a period of 20 years. A total of 18 OMOP CDM tables were implemented. A total of 17 local vocabularies were identified as being related to primary care and corresponded to patient characteristics (sex, location, year of birth, and race), units of measurement, biometric measures, laboratory test results, medical histories, and drug prescriptions. During semantic mapping, 10,221 primary care concepts were mapped to standard OHDSI concepts. Five queries were used to validate the OMOP CDM by comparing the results obtained after the completion of the transformations with the results obtained in the source software. Lastly, a prototype dashboard was developed to visualize the activity of the health center, the laboratory test results, and the drug prescription data.
UNASSIGNED: Primary care data from a French health care facility have been implemented into the OMOP CDM format. Data concerning demographics, units, measurements, and primary care consultation steps were already available in OHDSI vocabularies. Laboratory test results and drug prescription data were mapped to available vocabularies and structured in the final model. A dashboard application provided health care professionals with feedback on their practice.

UNASSIGNED: Dipeptidyl peptidase-4 (DPP4) inhibitors are frequently prescribed for patients with type 2 diabetes; however, their cost can pose a significant barrier for those with impaired kidney function. This study aimed to estimate the economic benefits of substituting non-renal dose-adjusted (NRDA) DPP4 inhibitors with renal dose-adjusted (RDA) DPP4 inhibitors in patients with both impaired kidney function and type 2 diabetes.
UNASSIGNED: This retrospective cohort study was conducted from January 1, 2012 to December 31, 2018, using data obtained from common data models of five medical centers in Korea. Model 1 applied the prescription pattern of participants with preserved kidney function to those with impaired kidney function. In contrast, model 2 replaced all NRDA DPP4 inhibitors with RDA DPP4 inhibitors, adjusting the doses of RDA DPP4 inhibitors based on individual kidney function. The primary outcome was the cost difference between the two models.
UNASSIGNED: In total, 67,964,996 prescription records were analyzed. NRDA DPP4 inhibitors were more frequently prescribed to patients with impaired kidney function than in those with preserved kidney function (25.7%, 51.3%, 64.3%, and 71.6% in patients with estimated glomerular filtration rates [eGFRs] of ≥60, <60, <45, and <30 mL/min/1.73 m2, respectively). When model 1 was applied, the cost savings per year were 7.6% for eGFR <60 mL/min/1.73 m2 and 30.4% for eGFR <30 mL/min/1.73 m2. According to model 2, 15.4% to 51.2% per year could be saved depending on kidney impairment severity.
UNASSIGNED: Adjusting the doses of RDA DPP4 inhibitors based on individual kidney function could alleviate the economic burden associated with medical expenses.

Common data models provide a standardized way to represent data used in federated learning tasks. The aim of this review was to explore the development and use of common data models to harmonize electronic health record data in health research. The data search yielded 724 records, of which 19 were included for this study. None of the research focused on nursing specific topics. All studies either utilized the Observational Medical Outcomes Partnership (OMOP) common data model, or developed a model partly based on the OMOP. A roadmap to guide research for the development of common data models for federated learning are warranted.

OBJECTIVE: Despite easy-to-use tools like the Cohort Builder, using All of Us Research Program data for complex research questions requires a relatively high level of technical expertise. We aimed to increase research and training capacity and reduce barriers to entry for the All of Us community through an R package, allofus. In this article, we describe functions that address common challenges we encountered while working with All of Us Research Program data, and we demonstrate this functionality with an example of creating a cohort of All of Us participants by synthesizing electronic health record and survey data with time dependencies.
BACKGROUND: All of Us Research Program data are widely available to health researchers. The allofus R package is aimed at a wide range of researchers who wish to conduct complex analyses using best practices for reproducibility and transparency, and who have a range of experience using R. Because the All of Us data are transformed into the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM), researchers familiar with existing OMOP CDM tools or who wish to conduct network studies in conjunction with other OMOP CDM data will also find value in the package.
METHODS: We developed an initial set of functions that solve problems we experienced across survey and electronic health record data in our own research and in mentoring student projects. The package will continue to grow and develop with the All of Us Research Program. The allofus R package can help build community research capacity by increasing access to the All of Us Research Program data, the efficiency of its use, and the rigor and reproducibility of the resulting research.

UNASSIGNED: Acute kidney injury (AKI) is a marker of clinical deterioration and renal toxicity. While there are many studies offering prediction models for the early detection of AKI, those predicting AKI occurrence using distributed research network (DRN)-based time series data are rare.
UNASSIGNED: In this study, we aimed to detect the early occurrence of AKI by applying an interpretable long short-term memory (LSTM)-based model to hospital electronic health record (EHR)-based time series data in patients who took nephrotoxic drugs using a DRN.
UNASSIGNED: We conducted a multi-institutional retrospective cohort study of data from 6 hospitals using a DRN. For each institution, a patient-based data set was constructed using 5 drugs for AKI, and an interpretable multivariable LSTM (IMV-LSTM) model was used for training. This study used propensity score matching to mitigate differences in demographics and clinical characteristics. Additionally, the temporal attention values of the AKI prediction model\'s contribution variables were demonstrated for each institution and drug, with differences in highly important feature distributions between the case and control data confirmed using 1-way ANOVA.
UNASSIGNED: This study analyzed 8643 and 31,012 patients with and without AKI, respectively, across 6 hospitals. When analyzing the distribution of AKI onset, vancomycin showed an earlier onset (median 12, IQR 5-25 days), and acyclovir was the slowest compared to the other drugs (median 23, IQR 10-41 days). Our temporal deep learning model for AKI prediction performed well for most drugs. Acyclovir had the highest average area under the receiver operating characteristic curve score per drug (0.94), followed by acetaminophen (0.93), vancomycin (0.92), naproxen (0.90), and celecoxib (0.89). Based on the temporal attention values of the variables in the AKI prediction model, verified lymphocytes and calcvancomycin ium had the highest attention, whereas lymphocytes, albumin, and hemoglobin tended to decrease over time, and urine pH and prothrombin time tended to increase.
UNASSIGNED: Early surveillance of AKI outbreaks can be achieved by applying an IMV-LSTM based on time series data through an EHR-based DRN. This approach can help identify risk factors and enable early detection of adverse drug reactions when prescribing drugs that cause renal toxicity before AKI occurs.

The common data model (CDM) has found widespread application in healthcare studies, but its utilization in cancer research has been limited. This article describes the development and implementation strategy for Cancer Clinical Library Databases (CCLDs), which are standardized cancer-specific databases established under the Korea-Clinical Data Utilization Network for Research Excellence (K-CURE) project by the Korean Ministry of Health and Welfare. Fifteen leading hospitals and fourteen academic associations in Korea are engaged in constructing CCLDs for 10 primary cancer types. For each cancer type-specific CCLD, cancer data experts determine key clinical data items essential for cancer research, standardize these items across cancer types, and create a standardized schema. Comprehensive clinical records covering diagnosis, treatment, and outcomes, with annual updates, are collected for each cancer patient in the target population, and quality control is based on six-sigma standards. To protect patient privacy, CCLDs follow stringent data security guidelines by pseudonymizing personal identification information and operating within a closed analysis environment. Researchers can apply for access to CCLD data through the K-CURE portal, which is subject to Institutional Review Board and Data Review Board approval. The CCLD is considered a pioneering standardized cancer-specific database, significantly representing Korea\'s cancer data. It is expected to overcome limitations of previous CDMs and provide a valuable resource for multicenter cancer research in Korea.

BACKGROUND: Digital transformation, particularly the integration of medical imaging with clinical data, is vital in personalized medicine. The Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) standardizes health data. However, integrating medical imaging remains a challenge.
OBJECTIVE: This study proposes a method for combining medical imaging data with the OMOP CDM to improve multimodal research.
METHODS: Our approach included the analysis and selection of digital imaging and communications in medicine header tags, validation of data formats, and alignment according to the OMOP CDM framework. The Fast Healthcare Interoperability Resources ImagingStudy profile guided our consistency in column naming and definitions. Imaging Common Data Model (I-CDM), constructed using the entity-attribute-value model, facilitates scalable and efficient medical imaging data management. For patients with lung cancer diagnosed between 2010 and 2017, we introduced 4 new tables-IMAGING_STUDY, IMAGING_SERIES, IMAGING_ANNOTATION, and FILEPATH-to standardize various imaging-related data and link to clinical data.
RESULTS: This framework underscores the effectiveness of I-CDM in enhancing our understanding of lung cancer diagnostics and treatment strategies. The implementation of the I-CDM tables enabled the structured organization of a comprehensive data set, including 282,098 IMAGING_STUDY, 5,674,425 IMAGING_SERIES, and 48,536 IMAGING_ANNOTATION records, illustrating the extensive scope and depth of the approach. A scenario-based analysis using actual data from patients with lung cancer underscored the feasibility of our approach. A data quality check applying 44 specific rules confirmed the high integrity of the constructed data set, with all checks successfully passed, underscoring the reliability of our findings.
CONCLUSIONS: These findings indicate that I-CDM can improve the integration and analysis of medical imaging and clinical data. By addressing the challenges in data standardization and management, our approach contributes toward enhancing diagnostics and treatment strategies. Future research should expand the application of I-CDM to diverse disease populations and explore its wide-ranging utility for medical conditions.

BACKGROUND: Chronic disease management is a major health issue worldwide. With the paradigm shift to preventive medicine, disease prediction modeling using machine learning is gaining importance for precise and accurate medical judgement.
OBJECTIVE: This study aimed to develop high-performance prediction models for 4 chronic diseases using the common data model (CDM) and machine learning and to confirm the possibility for the extension of the proposed models.
METHODS: In this study, 4 major chronic diseases-namely, diabetes, hypertension, hyperlipidemia, and cardiovascular disease-were selected, and a model for predicting their occurrence within 10 years was developed. For model development, the Atlas analysis tool was used to define the chronic disease to be predicted, and data were extracted from the CDM according to the defined conditions. A model for predicting each disease was built with 4 algorithms verified in previous studies, and the performance was compared after applying a grid search.
RESULTS: For the prediction of each disease, we applied 4 algorithms (logistic regression, gradient boosting, random forest, and extreme gradient boosting), and all models show greater than 80% accuracy. As compared to the optimized model\'s performance, extreme gradient boosting presented the highest predictive performance for the 4 diseases (diabetes, hypertension, hyperlipidemia, and cardiovascular disease) with 80% or greater and from 0.84 to 0.93 in area under the curve standards.
CONCLUSIONS: This study demonstrates the possibility for the preemptive management of chronic diseases by predicting the occurrence of chronic diseases using the CDM and machine learning. With these models, the risk of developing major chronic diseases within 10 years can be demonstrated by identifying health risk factors using our chronic disease prediction machine learning model developed with the real-world data-based CDM and National Health Insurance Corporation examination data that individuals can easily obtain.