Observational Medical Outcomes Partnership Research Articles

Taipei Medical University Clinical Research Database: a collaborative hospital EHR database aligned with international common data standards

ObjectiveThe objective of this paper is to provide a comprehensive overview of the development and features of the Taipei Medical University Clinical Research Database (TMUCRD), a repository of real-world data...

The prevalence of major depressive disorder in people with HIV: Results from the All of Us Research Program.

The All of Us (AoU) Research Program is a national-scale effort to build a dataset to help transform the future of health research by equipping researchers with comprehensive health data from diverse populations, especially those underrepresented in biomedical research. Our objectives were to evaluate the burden of HIV and major depressive disorder (MDD) in underrepresented groups and the frequency of the HIV/MDD comorbidity. We conducted a cross-sectional analysis combining collected survey and electronic health record (EHR) data. We ascertained HIV and MDD cases using Observational Medical Outcomes Partnership codes. We used multivariable logistic regression to obtain the odds ratio of HIV in AoU participants and MDD in AoU participants with HIV. The latest AoU data release includes 412 211 participants: 254 700 have at least one medical condition concept in their EHR, of whom 5193 (1.3%) had HIV, and 2238 (43%) of those with HIV had a diagnosis of MDD. Black AoU participants had approximately 4.58 times the odds of having an HIV diagnosis compared with the combined odds of all other racial groups. AoU participants with HIV were more likely to have MDD (p = 0.001) than were participants without HIV. Among AoU participants, Black individuals have a disproportionately high burden of HIV, pointing to underlying factors such as social determinants of health, limited access to healthcare or prevention resources, and potential systemic biases that contribute to these differences. In addition, HIV is a risk factor for mental health issues like MDD. Further data collection from people with HIV will elucidate contributing factors and the need for interventions.

Research protocol for an observational health data analysis to assess the applicability of randomized controlled trials focusing on newly diagnosed metastatic prostate cancer using real-world data: PIONEER IMI’s “big data for better outcomes” program

Background: Metastatic prostate cancer (PCa) constitutes ~5% of all new PCa diagnoses in Western countries. For most cases, primary consideration should be given to systemic therapies as the first-line approach based on evidence from randomized controlled trials (RCTs). Despite the importance of RCTs as the pinnacle of evidence in modern medicine, concerns have been raised about their applicability to real-life scenarios. These trials often feature participants who are younger with better performance statuses and prognoses compared to their real-world counterparts. The PIONEER project falls under the Innovative Medicine Initiative’s (IMI) “Big Data for Better Outcomes” initiative, aimed at revolutionizing PCa care in Europe. The central focus lies in improving cancer-related outcomes, enhancing health system efficiency, and elevating the quality of health and social care. This study endeavours to evaluate the generalizability of RCT findings concerning newly diagnosed metastatic PCa. Methods: A systematic review of the literature will be conducted to compile patient characteristics from RCTs addressing this subject within the past decade. To create a real-world benchmark, patients with recently diagnosed metastatic PCa from a network of population-based databases will serve as a comparison group. The objective is to assess the applicability of RCT results in two ways. First, a comparison will be made between the characteristics of patients with newly diagnosed metastatic PCa enroled in RCTs and those with the same condition included in our databases which might represent the real-world setting. Second, an evaluation will be undertaken to determine the proportion of real-world patients with newly diagnosed metastatic PCa who meet the criteria for RCT enrolment. This study will rely on extensive observational data, primarily sourced from population-based registries, electronic health records, and insurance claims data. The study cohort is established upon routinely gathered healthcare data, meticulously mapped to the Observational Medical Outcomes Partnership Common Data Model.

Data Resource Profile: Health Insurance Review and Assessment Service Covid-19 Observational Medical Outcomes Partnership (HIRA Covid-19 OMOP) database in South Korea.

Data Resource Profile: Health Insurance Review and Assessment Service Covid-19 Observational Medical Outcomes Partnership (HIRA Covid-19 OMOP) database in South Korea.

Learning from conect4children: A Collaborative Approach towards Standardisation of Disease-Specific Paediatric Research Data

The conect4children (c4c) initiative was established to facilitate the development of new drugs and other therapies for paediatric patients. It is widely recognised that there are not enough medicines tested for all relevant ages of the paediatric population. To overcome this, it is imperative that clinical data from different sources are interoperable and can be pooled for larger post hoc studies. c4c has collaborated with the Clinical Data Interchange Standards Consortium (CDISC) to develop cross-cutting data resources that build on existing CDISC standards in an effort to standardise paediatric data. The natural next step was an extension to disease-specific data items. c4c brought together several existing initiatives and resources relevant to disease-specific data and analysed their use for standardising disease-specific data in clinical trials. Several case studies that combined disease-specific data from multiple trials have demonstrated the need for disease-specific data standardisation. We identified three relevant initiatives. These include European Reference Networks, European Joint Programme on Rare Diseases, and Pistoia Alliance. Other resources reviewed were National Cancer Institute Enterprise Vocabulary Services, CDISC standards, pharmaceutical company-specific data dictionaries, Human Phenotype Ontology, Phenopackets, Unified Registry for Inherited Metabolic Disorders, Orphacodes, Rare Disease Cures Accelerator-Data and Analytics Platform (RDCA-DAP), and Observational Medical Outcomes Partnership. The collaborative partners associated with these resources were also reviewed briefly. A plan of action focussed on collaboration was generated for standardising disease-specific paediatric clinical trial data. A paediatric data standards multistakeholder and multi-project user group was established to guide the remaining actions—FAIRification of metadata, a Phenopackets pilot with RDCA-DAP, applying Orphacodes to case report forms of clinical trials, introducing CDISC standards into European Reference Networks, testing of the CDISC Pediatric User Guide using data from the mentioned resources and organisation of further workshops and educational materials.

RecruIT: A cloud-native clinical trial recruitment support system based on Health Level 7 Fast Healthcare Interoperability Resources (HL7 FHIR) and the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM)

BackgroundClinical trials (CTs) are foundational to the advancement of evidence-based medicine and recruiting a sufficient number of participants is one of the crucial steps to their successful conduct. Yet, poor recruitment remains the most frequent reason for premature discontinuation or costly extension of clinical trials. MethodsWe designed and implemented a novel, open-source software system to support the recruitment process in clinical trials by generating automatic recruitment recommendations. The development is guided by modern, cloud-native design principles and based on Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) as an interoperability standard with the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) being used as a source of patient data. We evaluated the usability using the system usability scale (SUS) after deploying the application for use by study personnel. ResultsThe implementation is based on the OMOP CDM as a repository of patient data that is continuously queried for possible trial candidates based on given clinical trial eligibility criteria. A web-based screening list can be used to display the candidates and email notifications about possible new trial participants can be sent automatically. All interactions between services use HL7 FHIR as the communication standard. The system can be installed using standard container technology and supports more sophisticated deployments on Kubernetes clusters. End-users (n = 19) rated the system with a SUS score of 79.9/100. ConclusionWe contribute a novel, open-source implementation to support the patient recruitment process in clinical trials that can be deployed using state-of-the art technologies. According to the SUS score, the system provides good usability.

76 Lessons learned during implementation of OMOP common data model across multiple health systems

OBJECTIVES/GOALS: Adoption of the Observational Medical Outcomes Partnership (OMOP) common data model promises to transform large-scale observational health research. However, there are diverse challenges for operationalizing OMOP in terms of interoperability and technical skills among coordinating centers throughout the US. METHODS/STUDY POPULATION: A team from the Critical Path Institute (C-Path) collaborated with the informatics team members at Johns Hopkins to provide technical support to participating sites as part of the Extract, Transform, and Load (ETL) process linking existing concepts to OMOP concepts. Health systems met regularly via teleconference to review challenges and progress in ETL process. Sites were responsible for performing the local ETL process with assistance and securely provisioning de-identified data as part of the CURE ID program. RESULTS/ANTICIPATED RESULTS: More than twenty health systems participated in the CURE ID effort.Laboratory measures, basic demographics, disease diagnoses and problem list were more easily mapped to OMOP concepts by CURE ID partner institutions. Outcomes, social determinants of health, medical devices, and specific treatments were less easily characterized as part of the project. Concepts within the medical record presented very different technical challenges in terms of representation. There is a lack of standardization in OMOP implementation even among centers using the same electronic medical health record. Readiness to adopt OMOP varied across the institutions who participated. Health systems achieved variable level of coverage using OMOP medical concepts as part of the initiative. DISCUSSION/SIGNIFICANCE: Adoption of OMOP involves local stakeholder knowledge and implementation. Variable complexity of health concepts contributed to variable coverage. Documentation and support require extensive time and effort. Open-source software can be technically challenging. Interoperability of secure data systems presents unique problems.

Use of Recommended Neurodiagnostic Evaluation Among Patients With Drug-Resistant Epilepsy

Interdisciplinary practice parameters recommend that patients with drug-resistant epilepsy (DRE) undergo comprehensive neurodiagnostic evaluation, including presurgical assessment. Reporting from specialized centers suggests long delays to referral and underuse of surgery; however, longitudinal data are limited to characterize neurodiagnostic evaluation among patients with DRE in more diverse US settings and populations. To examine the rate and factors associated with neurodiagnostic studies and comprehensive evaluation among patients with DRE within 3 US cohorts. A retrospective cross-sectional study was conducted using the Observational Medical Outcomes Partnership Common Data Model including US multistate Medicaid data, commercial claims data, and Columbia University Medical Center (CUMC) electronic health record data. Patients meeting a validated computable phenotype algorithm for DRE between January 1, 2015, and April 1, 2020, were included. No eligible participants were excluded. Demographic and clinical variables were queried. The proportion of patients receiving a composite proxy for comprehensive neurodiagnostic evaluation, including (1) magnetic resonance or other advanced brain imaging, (2) video electroencephalography, and (3) neuropsychological evaluation within 2 years of meeting the inclusion criteria. A total of 33 542 patients with DRE were included in the Medicaid cohort, 22 496 in the commercial insurance cohort, and 2741 in the CUMC database. A total of 31 516 patients (53.6%) were women. The proportion of patients meeting the comprehensive evaluation main outcome in the Medicaid cohort was 4.5% (n = 1520); in the commercial insurance cohort, 8.0% (n = 1796); and in the CUMC cohort, 14.3% (n = 393). Video electroencephalography (24.9% Medicaid, 28.4% commercial, 63.2% CUMC) and magnetic resonance imaging of the brain (35.6% Medicaid, 43.4% commercial, 52.6% CUMC) were performed more regularly than neuropsychological evaluation (13.0% Medicaid, 16.6% commercial, 19.2% CUMC) or advanced imaging (3.2% Medicaid, 5.4% commercial, 13.1% CUMC). Factors independently associated with greater odds of evaluation across all 3 data sets included the number of inpatient and outpatient nonemergency epilepsy visits and focal rather than generalized epilepsy. The findings of this study suggest there is a gap in the use of diagnostic studies to evaluate patients with DRE. Care setting, insurance type, frequency of nonemergency visits, and epilepsy type are all associated with evaluation. A common data model can be used to measure adherence with best practices across a variety of observational data sources.

Correlation of Socioeconomic and Environmental Factors With Incidence of Crohn Disease in Children and Adolescents: Systematic Review and Meta-Regression.

The worldwide incidence of Crohn disease (CD) in childhood and adolescence has an increasing trend, with significant differences between different geographic regions and individual countries. This includes an increase in the incidence of CD in countries and geographic regions where CD was not previously prevalent. In response to the increasing incidence, the pediatric care landscape is facing growing challenges. This systematic review and meta-analysis were undertaken to comprehensively delineate the incidence rates of CD in pediatric populations across different countries and to explore potential influencing factors. We performed a systematic review of PubMed and Embase (via Ovid) for studies from January 1, 1970, to December 31, 2019. In addition, a manual search was performed in relevant and previously published reviews. The results were evaluated quantitatively. For this purpose, random effects meta-analyses and meta-regressions were performed to investigate the overall incidence rate and possible factors influencing the incidence. A qualitative synthesis of 74 studies was performed, with 72 studies included in the meta-analyses and 52 in the meta-regressions. The results of our meta-analysis showed significant heterogeneity between the individual studies, which cannot be explained by a sample effect alone. Our findings showed geographical differences in incidence rates, which increased with increasing distance from the equator, although no global temporal trend was apparent. The meta-regression analysis also identified geographic location, UV index, and Human Development Index as significant moderators associated with CD incidence. Our results suggest that pediatric CD incidence has increased in many countries since 1970 but varies widely with geographic location, which may pose challenges to the respective health care systems. We identified geographic, environmental, and socioeconomic factors that contribute to the observed heterogeneity in incidence rates. These results can serve as a basis for future research. To this end, implementations of internationally standardized and interoperable registries combined with the dissemination of health data through federated networks based on a common data model, such as the Observational Medical Outcomes Partnership, would be beneficial. This would deepen the understanding of CD and promote evidence-based approaches to preventive and interventional strategies as well as inform public health policies aimed at addressing the increasing burden of CD in children and adolescents. PROSPERO International prospective register of systematic reviews CRD42020168644; https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=168644. RR2-10.1136/bmjopen-2020-037669.

Abstract 3558: An integrated data platform to support the international alliance for cancer early detection

Abstract Cancer early detection is one of the most critical areas of cancer research, as it offers the greatest potential for improving patient outcomes. The International Alliance for Cancer Early Detection (ACED) is a global partnership of world-leading cancer research institutions in the UK and US, established in 2019 to accelerate and revolutionize research in this field. ACED brings together the expertise of the Canary Center at Stanford University, the University of Cambridge, the Knight Cancer Institute at Oregon Health and Sciences University, University College London, and the University of Manchester, together with Cancer Research UK, with the goal of catalyzing new collaborations and research in the field of early detection. One of the major challenges to enabling international collaborations across different institutions is the ability to collect, share and discover datasets between researchers and institutions. To enable collaboration on innovative data science, fundamental functions include, 1) controlled data sharing mechanisms; 2) structured metadata to enable data exploration and data discovery; and 3) enabling easy computational access to that data. To advance researchers' collaboration, ACED began development of an Integrated Data Platform (IDP). The ACED-IDP is based on the Gen3 software platform developed by the University of Chicago's Center for Translational Data Science. Based on software systems originally developed for the NCI's Genomic Data Commons, Gen3 has been used in several other data projects including The Blood Profiling Atlas in Cancer (BloodPAC), Australian BioCommons and numerous other research data platforms. The unique nature of ACED required unique innovations to be made for the development of the IDP. Each of the member institutions within the alliance has different existing computer infrastructures, separate authentication platforms and heterogeneous data types forming the basis of their research. The IDP sought a cloud-ready strategy, while still being cognizant of the extreme costs associated with cloud egress fees that hamper researchers' ability to download data. Additions were made to the Gen3 platform to allow for hybrid cloud support, allowing on-premises as well as cloud object storage systems to be linked to the platform. This innovation permits each institution to share files using the mechanisms that they see fit. To unify the various datasets, the standard Gen3 schema was replaced with one derived from the Fast Healthcare Interoperability Resources (FHIR) standard. To support import from clinical data sets, tooling to enable import and export Observational Medical Outcomes Partnership (OMOP) data has been integrated. With this platform in place, we hope to advance international collaborations and accelerate early cancer detection research. Citation Format: Brian Walsh, Liam Beckman, JD Burchett, Matthew Peterkort, Jordan Lee, Michael Fitzsimons, Peter Vassilatos, Binam Bajracharya, Craig Barnes, Jawad Qureshi, Robert Grossman, Carrie Yakura, Yaozhi Lu, Sarah Burge, Daniel Kelberman, Erin Watson, Kyle Ellrott. An integrated data platform to support the international alliance for cancer early detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3558.

Real-world evidence of constipation and laxative use in the Korean population with chronic kidney disease from a common data model

Constipation is a highly prevalent gastrointestinal disorder in patients with chronic kidney disease (CKD). However, our understanding of its epidemiology and management in CKD is limited. We aimed to explore real-world data on constipation and laxative use in patients with CKD in a nationwide population-based cohort from the Korean Health Insurance Review and Assessment-National Patient Sample database. This study analyzed retrospective health claims data in Korea from 2012 to 2017 that were transformed into the Observational Medical Outcomes Partnership Common Data Model. The pooled proportion of constipation diagnoses was 30.5% in all patients with CKD and 15.9%, 16.5%, 17.4%, 29.9%, and 43.3% in patients with CKD stages 1–5, respectively, suggesting a higher prevalence in advanced CKD. Patients receiving peritoneal dialysis or hemodialysis had the highest prevalence of constipation, while transplant recipients showed a prevalence comparable to that of patients with early CKD. Patients with CKD had a significantly higher risk of constipation than age- and sex-matched non-CKD individuals (range of odds ratio [OR]:1.66–1.90). Laxative prescribing patterns differed by CKD severity. Osmotic agents were prescribed in more than half of patients with advanced CKD, while magnesium salts and bulking agents were prescribed less frequently. The CKD patients with constipation were more likely to be prescribed constipation-inducing medications, including antipsychotic and neurological medications. Our findings provide real-world constipation and laxative prescription status in the Korean CKD population, revealing a significantly higher risk of constipation and different laxative prescribing patterns in patients with CKD.

Prediction of 30-day, 90-day, and 1-year mortality after colorectal cancer surgery using a data-driven approach

PurposeTo develop prediction models for short-term mortality risk assessment following colorectal cancer surgery.MethodsData was harmonized from four Danish observational health databases into the Observational Medical Outcomes Partnership Common Data Model. With a data-driven approach using the Least Absolute Shrinkage and Selection Operator logistic regression on preoperative data, we developed 30-day, 90-day, and 1-year mortality prediction models. We assessed discriminative performance using the area under the receiver operating characteristic and precision-recall curve and calibration using calibration slope, intercept, and calibration-in-the-large. We additionally assessed model performance in subgroups of curative, palliative, elective, and emergency surgery.ResultsA total of 57,521 patients were included in the study population, 51.1% male and with a median age of 72 years. The model showed good discrimination with an area under the receiver operating characteristic curve of 0.88, 0.878, and 0.861 for 30-day, 90-day, and 1-year mortality, respectively, and a calibration-in-the-large of 1.01, 0.99, and 0.99. The overall incidence of mortality were 4.48% for 30-day mortality, 6.64% for 90-day mortality, and 12.8% for 1-year mortality, respectively. Subgroup analysis showed no improvement of discrimination or calibration when separating the cohort into cohorts of elective surgery, emergency surgery, curative surgery, and palliative surgery.ConclusionWe were able to train prediction models for the risk of short-term mortality on a data set of four combined national health databases with good discrimination and calibration. We found that one cohort including all operated patients resulted in better performing models than cohorts based on several subgroups.

Conceptual design of a generic data harmonization process for OMOP common data model

BackgroundTo gain insight into the real-life care of patients in the healthcare system, data from hospital information systems and insurance systems are required. Consequently, linking clinical data with claims data is necessary. To ensure their syntactic and semantic interoperability, the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) from the Observational Health Data Sciences and Informatics (OHDSI) community was chosen. However, there is no detailed guide that would allow researchers to follow a generic process for data harmonization, i.e. the transformation of local source data into the standardized OMOP CDM format. Thus, the aim of this paper is to conceptualize a generic data harmonization process for OMOP CDM.MethodsFor this purpose, we conducted a literature review focusing on publications that address the harmonization of clinical or claims data in OMOP CDM. Subsequently, the process steps used and their chronological order as well as applied OHDSI tools were extracted for each included publication. The results were then compared to derive a generic sequence of the process steps.ResultsFrom 23 publications included, a generic data harmonization process for OMOP CDM was conceptualized, consisting of nine process steps: dataset specification, data profiling, vocabulary identification, coverage analysis of vocabularies, semantic mapping, structural mapping, extract-transform-load-process, qualitative and quantitative data quality analysis. Furthermore, we identified seven OHDSI tools which supported five of the process steps.ConclusionsThe generic data harmonization process can be used as a step-by-step guide to assist other researchers in harmonizing source data in OMOP CDM.

Evaluating MedDRA-to-ICD terminology mappings

BackgroundIn this era of big data, data harmonization is an important step to ensure reproducible, scalable, and collaborative research. Thus, terminology mapping is a necessary step to harmonize heterogeneous data. Take the Medical Dictionary for Regulatory Activities (MedDRA) and International Classification of Diseases (ICD) for example, the mapping between them is essential for drug safety and pharmacovigilance research. Our main objective is to provide a quantitative and qualitative analysis of the mapping status between MedDRA and ICD.We focus on evaluating the current mapping status between MedDRA and ICD through the Unified Medical Language System (UMLS) and Observational Medical Outcomes Partnership Common Data Model (OMOP CDM). We summarized the current mapping statistics and evaluated the quality of the current MedDRA-ICD mapping; for unmapped terms, we used our self-developed algorithm to rank the best possible mapping candidates for additional mapping coverage.ResultsThe identified MedDRA-ICD mapped pairs cover 27.23% of the overall MedDRA preferred terms (PT). The systematic quality analysis demonstrated that, among the mapped pairs provided by UMLS, only 51.44% are considered an exact match. For the 2400 sampled unmapped terms, 56 of the 2400 MedDRA Preferred Terms (PT) could have exact match terms from ICD.ConclusionSome of the mapped pairs between MedDRA and ICD are not exact matches due to differences in granularity and focus. For 72% of the unmapped PT terms, the identified exact match pairs illustrate the possibility of identifying additional mapped pairs. Referring to its own mapping standard, some of the unmapped terms should qualify for the expansion of MedDRA to ICD mapping in UMLS.

Impact of COVID-19 on the development of major mental disorders in patients visiting a university hospital: a retrospective observational study.

This study aimed to investigate the impact of coronavirus disease 2019 (COVID-19) on the development of major mental disorders in patients visiting a university hospital. The study participants were patients with COVID-19 (n=5,006) and those without COVID-19 (n=367,162) registered in the database of Keimyung University Dongsan Hospital and standardized with the Observational Medical Outcomes Partnership Common Data Model. Data on major mental disorders that developed in both groups over the 5-year follow-up period were extracted using the FeederNet computer program. A multivariate Cox proportional hazards model was used to estimate the hazard ratio (HR) and 95% confidence interval (CI) for the incidence of major mental disorders. The incidences of dementia and sleep, anxiety, and depressive disorders were significantly higher in the COVID-19 group than in the control group. The incidence rates per 1,000 patient-years in the COVID-19 group vs. the control group were 12.71 vs. 3.76 for dementia, 17.42 vs. 7.91 for sleep disorders, 6.15 vs. 3.41 for anxiety disorders, and 8.30 vs. 5.78 for depressive disorders. There was no significant difference in the incidence of schizophrenia or bipolar disorder between the two groups. COVID-19 infection increased the risk of mental disorders in the following order: dementia (HR, 3.49; 95% CI, 2.45-4.98), sleep disorders (HR, 2.27; 95% CI, 1.76-2.91), anxiety disorders (HR, 1.90; 95% CI, 1.25-2.84), and depressive disorders (HR, 1.54; 95% CI, 1.09-2.15). This study showed that the major mental disorders associated with COVID-19 were dementia and sleep, anxiety, and depressive disorders.

Development of Medical Imaging Data Standardization for Imaging-Based Observational Research: OMOP Common Data Model Extension

The rapid growth of artificial intelligence (AI) and deep learning techniques require access to large inter-institutional cohorts of data to enable the development of robust models, e.g., targeting the identification of disease biomarkers and quantifying disease progression and treatment efficacy. The Observational Medical Outcomes Partnership Common Data Model (OMOP CDM) has been designed to accommodate a harmonized representation of observational healthcare data. This study proposes the Medical Imaging CDM (MI-CDM) extension, adding two new tables and two vocabularies to the OMOP CDM to address the structural and semantic requirements to support imaging research. The tables provide the capabilities of linking DICOM data sources as well as tracking the provenance of imaging features derived from those images. The implementation of the extension enables phenotype definitions using imaging features and expanding standardized computable imaging biomarkers. This proposal offers a comprehensive and unified approach for conducting imaging research and outcome studies utilizing imaging features.

A comparative patient-level prediction study in OMOP CDM: applicative potential and insights from synthetic data

The emergence of collaborations, which standardize and combine multiple clinical databases across different regions, provide a wealthy source of data, which is fundamental for clinical prediction models, such as patient-level predictions. With the aid of such large data pools, researchers are able to develop clinical prediction models for improved disease classification, risk assessment, and beyond. To fully utilize this potential, Machine Learning (ML) methods are commonly required to process these large amounts of data on disease-specific patient cohorts. As a consequence, the Observational Health Data Sciences and Informatics (OHDSI) collaborative develops a framework to facilitate the application of ML models for these standardized patient datasets by using the Observational Medical Outcomes Partnership (OMOP) common data model (CDM). In this study, we compare the feasibility of current web-based OHDSI approaches, namely ATLAS and “Patient-level Prediction” (PLP), against a native solution (R based) to conduct such ML-based patient-level prediction analyses in OMOP. This will enable potential users to select the most suitable approach for their investigation. Each of the applied ML solutions was individually utilized to solve the same patient-level prediction task. Both approaches went through an exemplary benchmarking analysis to assess the weaknesses and strengths of the PLP R-Package. In this work, the performance of this package was subsequently compared versus the commonly used native R-package called Machine Learning in R 3 (mlr3), and its sub-packages. The approaches were evaluated on performance, execution time, and ease of model implementation. The results show that the PLP package has shorter execution times, which indicates great scalability, as well as intuitive code implementation, and numerous possibilities for visualization. However, limitations in comparison to native packages were depicted in the implementation of specific ML classifiers (e.g., Lasso), which may result in a decreased performance for real-world prediction problems. The findings here contribute to the overall effort of developing ML-based prediction models on a clinical scale and provide a snapshot for future studies that explicitly aim to develop patient-level prediction models in OMOP CDM.

Feasibility of Applying the OMOP Common Data Model to Traditional Eastern Asian Medicine Dataset.

To evaluate the feasibility of applying the Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM) to databases of traditional East Asian medicine (TEAM), we composed a TEAM dataset and transformed it to the OMOP CDM. We found that some important TEAM information entities could not be transformed to the OMOP CDM (version 6.0) data fields. We suggest to develop data fields and guideline for transforming TEAM data to the OMOP CDM.

Health-Analytics Data to Evidence Suite (HADES): Open-Source Software for Observational Research.

The Health-Analytics Data to Evidence Suite (HADES) is an open-source software collection developed by Observational Health Data Sciences and Informatics (OHDSI). It executes directly against healthcare data such as electronic health records and administrative claims, that have been converted to the Observational Medical Outcomes Partnership (OMOP) Common Data Model. Using advanced analytics, HADES performs characterization, population-level causal effect estimation, and patient-level prediction, potentially across a federated data network, allowing patient-level data to remain locally while only aggregated statistics are shared. Designed to run across a wide array of technical environments, including different operating systems and database platforms, HADES uses continuous integration with a large set of unit tests to maintain reliability. HADES implements OHDSI best practices, and is used in almost all published OHDSI studies, including some that have directly informed regulatory decisions.

Development of Integrated Data Quality Management System for Observational Medical Outcomes Partnership Common Data Model.

The amount of research on the gathering and handling of healthcare data keeps growing. To support multi-center research, numerous institutions have sought to create a common data model (CDM). However, data quality issues continue to be a major obstacle in the development of CDM. To address these limitations, a data quality assessment system was created based on the representative data model OMOP CDM v5.3.1. Additionally, 2,433 advanced evaluation rules were created and incorporated into the system by mapping the rules of existing OMOP CDM quality assessment systems. The data quality of six hospitals was verified using the developed system and an overall error rate of 0.197% was confirmed. Finally, we proposed a plan for high-quality data generation and the evaluation of multi-center CDM quality.