Standardizing registry data to the OMOP Common Data Model: experience from three pulmonary hypertension databases

Biological markers and psychosocial factors predict chronic pain conditions

Chronic pain is a multifactorial condition presenting significant diagnostic and prognostic challenges. Biomarkers for the classification and the prediction of chronic pain are therefore critically needed. Here, in this multidataset study of over 523,000 participants, we applied machine learning to multidimensional biological data from the UK Biobank to identify biomarkers for 35 medical conditions associated with pain (for example, rheumatoid arthritis and gout) or self-reported chronic pain (for example, back pain and knee pain). Biomarkers derived from blood immunoassays, brain and bone imaging, and genetics were effective in predicting medical conditions associated with chronic pain (area under the curve (AUC) 0.62-0.87) but not self-reported pain (AUC 0.50-0.62). Notably, all biomarkers worked in synergy with psychosocial factors, accurately predicting both medical conditions (AUC 0.69-0.91) and self-reported pain (AUC 0.71-0.92). These findings underscore the necessity of adopting a holistic approach in the development of biomarkers to enhance their clinical utility.

Investigating CAR-T Treatment Access for Multiple Myeloma Patients Using Real-World Evidence

Objective

Multiple myeloma (MM) is the second most common hematologic malignancy in the U.S., with Black patients being diagnosed at twice the rate of White patients. MM treatment options are limited and ineffective, but CAR-T therapies show promise. However, their limited availability results in disparities in access. This study aimed to explore disparities in Multiple Myeloma disease risk and CAR-T therapy access.

Methods

Our study included a population-based cohort of 12,360 patients diagnosed with Multiple Myeloma who received more than one cancer therapy extracted from the University of California Health Data Warehouse (UCHDW) between January 2021 and November 2024. Regression models were used to compute odds ratio (OR) and 95% confidence intervals (CI) associating disease severity, UC-Location, and baseline demographics with CAR-T therapy access. The GPT-4 inference model was prompted with a zero-shot learning approach to analyze UCSF clinical notes with the following objectives: (1) Was CAR-T discussed? [yes/no], (2) Is the patient eligible for CAR-T? [yes/no/unclear], and (3) Provide the rationale for the eligibility determination.

Results

Our study included 12,360 patients (mean age 68.5 years, SD 12.8 years) treated for multiple myeloma across the University of California Health System, 320 of which received CAR-T (Table-1). Overall, 51.6% of MM patients identified as Male, and 48.4% as Female. Disease Severity was measured by the International Staging System (ISS) and was distributed by ISS Stage: I (65.3%), II (24.4%), III (2.8%), and None (7.5%). Patients treated at UC-1 (49.3%), and UC-2 (50.0%) were primarily diagnosed with Stage II, while patients at UC-3 (55.5%) were primarily diagnosed with Stage I. Our model indicated that patients who identified as Black or African American (OR= 0.33, [95% CI, 0.17-0.62) were less likely to receive CAR-T therapy when compared to White patients. Patients treated at UC-3 with predominantly Black or African American patients (OR = 0.42, [95% CI, 0.30-0.59]) were less likely to receive CAR-T therapy when compared to UC-1. We identified CAR-T eligibility for 270 UCSF patients and found those who identified as other Pacific Islander had the highest rate of eligibility without discussions at 50%, followed by Black or African American (4.2%), Asian (3.2%), and White (0.6%).

Conclusion and Relevance

This study emphasizes the influence of race and UC-Location on disparities in CAR-T therapy access.

Secular trends in heat related illness and excess sun exposure rates across climatic zones in the United States from 2017 to 2022

Heat waves are a major public health challenge, yet the link between heat-related illness (HRI) and regional climate and geography is underexplored. We examined HRI and excess sun exposure incidence rates (IR) [95% confidence interval (CI) per 100,000 person-years], and their correlation with regional maximum temperatures across 9 US climatic zones 33,603,572 individuals were followed from 2017 to 2022. We observed 10,652 individuals with HRI diagnosis (median age: 49 years, 62.3% male). Seasonal peaks occurred during summer: highest overall IR (130.97 [119.93-142.75]) was recorded in July 2019, highest regional IR was reported in the South (186.04 [117.93-279.15]) during 2020. Strongest correlations between monthly maximum temperature and incidence of HRI were observed in the West (Pearson Correlation Coefficient (cor) = 0.854) and Southwest (cor = 0.832). In contrast, we observed 131,204 individuals with excess sun exposure (predominantly older adults [median age: 67 years], 52.3% female, 30% with history of cancer). Overall IR for sun exposure peaked in March 2021 (664.31 [644.84-684.21]) and lacked a consistent seasonal pattern. Sun exposure exhibited weaker correlations with regional temperatures, even in high-temperature regions like the West (cor = 0.305). These data indicate regional variations in HRI. With distinct at-risk groups for HRI and sun exposure, targeted regional interventions may be beneficial, such as heat safety protocols to reduce HRI risk and sun protection campaigns for older adults to mitigate sun exposure risk.

Real-World Type 2 Diabetes Second-Line Treatment Allocation Among Patients

Objective

This study aimed to evaluate the impact of socioeconomic disparities on the allocation of second-line treatments among patients with type 2 diabetes (T2D).

Materials and Methods

We conducted an observational study using real-world data from over 9 million patients across five University of California Health centers. The study included patients who initiated a second-line T2D medication after metformin, with hemoglobin A1c (HbA1c) measurements within ±7 days of treatment initiation from 2012 through September 2024. Multinomial regression models assessed the association between socioeconomic status and second-line treatment choices. Additionally, we used the GPT-4 large language model with a zero-shot learning approach to analyze 270 clinical notes from 105 UCSF patients. GPT-4 identified adverse social determinants of health (SDOH) across six domains: transportation, housing, relationships, patients with children, support, and employment.

Results

Among 15,090 patients (56.7% male, 43.3% female; mean age 59.3 years; mean HbA1c 8.91%), second-line treatments included sulfonylureas (SUs; n = 6,732), DPP4 inhibitors (n = 2,918), GLP-1 receptor agonists (n = 2,736), and SGLT2 inhibitors (n = 2,704). Patients from lower socioeconomic neighborhoods were more likely to receive SUs over other medications: DPP4i (OR = 0.96, [95% CI, 0.95-0.98]), GLP-1RA (OR = 0.94, [95% CI, 0.92-0.96]), SGLT2i (OR = 0.95, [95% CI, 0.93-0.97]). In UCSF clinical notes, we identified adverse SDOH including housing (n=8), transportation (n=1), relationships (n=22), employment (n=12), support (n=1), and patients with children (n=25).

Conclusions

Socioeconomic factors influence second-line T2D treatment choices. Addressing these disparities is essential to ensuring equitable access to advanced T2D therapies.

Implementing a Common Data Model in Ophthalmology: Mapping Structured Electronic Health Record Ophthalmic Examination Data to Standard Vocabularies

Objective

To identify and characterize concept coverage gaps of ophthalmology examination data elements within the Cerner Millennium electronic health record (EHR) implementations by the Observational Health Data Sciences and Informatics Observational Medical Outcomes Partnership (OMOP) common data model (CDM).

Design

Analysis of data elements in EHRs.

Subjects

Not applicable.

Methods

Source eye examination data elements from the default Cerner Model Experience EHR and a local implementation of the Cerner Millennium EHR were extracted, classified into one of 8 subject categories, and mapped to the semantically closest standard concept in the OMOP CDM. Mappings were categorized as exact, if the data element and OMOP concept represented equivalent information, wider, if the OMOP concept was missing conceptual granularity, narrower, if the OMOP concept introduced excess information, and unmatched, if no standard concept adequately represented the data element. Descriptive statistics and qualitative analysis were used to describe the concept coverage for each subject category.

Main Outcome Measures

Concept coverage gaps in 8 ophthalmology subject categories of data elements by the OMOP CDM.

Results

There were 409 and 947 ophthalmology data elements in the default and local Cerner modules, respectively. Of the 409 mappings in the default Cerner module, 25% (n = 102) were exact, 53% (n = 217) were wider, 3% (n = 11) were narrower, and 19% (n = 79) were unmatched. In the local Cerner module, 18% (n = 173) of mappings were exact, 54% (n = 514) were wider, 1% (n = 10) were narrower, and 26% (n = 250) were unmatched. The largest coverage gaps were seen in the local Cerner module under the visual acuity, sensorimotor testing, and refraction categories, with 95%, 95%, and 81% of data elements in each respective category having mappings that were not exact. Concept coverage gaps spanned all 8 categories in both EHR implementations.

Conclusions

Considerable coverage gaps by the OMOP CDM exist in all areas of the ophthalmology examination, which should be addressed to improve the OMOP CDM's effectiveness in ophthalmic research. We identify specific subject categories that may benefit from increased granularity in the OMOP CDM and provide suggestions for facilitating consistency of standard concepts, with the goal of improving data standards in ophthalmology.

Financial Disclosures

Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Harmonizing population health data into OMOP common data model: a demonstration using COVID-19 sero-surveillance data from Nairobi Urban Health and Demographic Surveillance System

Background

Observational health data are collected in different formats and structures, making it challenging to analyze with common tools. The Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM) is a standardized data model that can harmonize observational health data.

Objective

This paper demonstrates the use of the OMOP CDM to harmonize COVID-19 sero-surveillance data from the Nairobi Urban Health and Demographic Surveillance System (HDSS).

Methods

In this study, we extracted data from the Nairobi Urban HDSS COVID-19 sero-surveillance database and mapped it to the OMOP CDM. We used open-source Observational Health Data Sciences and Informatics (OHDSI) tools like WhiteRabbit, RabbitInAHat, and USAGI. The steps included data profiling (scanning), mapping the vocabularies using the offline USAGI and online ATHENA, and designing the extract, transform, and load (ETL) process using RabbitInAHat. The ETL process was implemented using Pentaho Data Integration community edition software and structured query language (SQL). The target OMOP CDM can now be used to analyze the prevalence of COVID-19 antibodies in the Nairobi Urban HDSS population.

Results

We successfully mapped the Nairobi Urban HDSS COVID-19 sero-surveillance data to the OMOP CDM. The standardized dataset included information on demographics, COVID-19 symptoms, vaccination, and COVID-19 antibody test results.

Conclusions

The OMOP CDM is a valuable tool for harmonizing observational health data. Using the OMOP CDM facilitates the sharing and analysis of observational health data, leading to a better understanding of disease conditions and trends and improving evidence-based population health strategies.

Making the Case for an International Childhood Cancer Data Partnership

Childhood cancers are a heterogeneous group of rare diseases, accounting for less than 2% of all cancers diagnosed worldwide. Most countries, therefore, do not have enough cases to provide robust information on epidemiology, treatment, and late effects, especially for rarer types of cancer. Thus, only through a concerted effort to share data internationally will we be able to answer research questions that could not otherwise be answered. With this goal in mind, the U.S. National Cancer Institute and the French National Cancer Institute co-sponsored the Paris Conference for an International Childhood Cancer Data Partnership in November 2023. This meeting convened more than 200 participants from 17 countries to address complex challenges in pediatric cancer research and data sharing. This Commentary delves into some key topics discussed during the Paris Conference and describes pilots that will help move this international effort forward. Main topics presented include: 1) the wide variation in interpreting the European Union's General Data Protection Regulation among Member States; 2) obstacles with transferring personal health data outside of the European Union; 3) standardization and harmonization, including common data models; and 4) novel approaches to data sharing such as federated querying and federated learning. We finally provide a brief description of three ongoing pilot projects. The International Childhood Cancer Data Partnership is the first step in developing a process to better support pediatric cancer research internationally through combining data from multiple countries.

Repeatable process for extracting health data from HL7 CDA documents

OBJECTIVE

This study aims to address the gap in the literature on converting real-world Clinical Document Architecture (CDA) data into the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM), focusing on the initial steps preceding the mapping phase. We highlight the importance of a repeatable Extract-Transform-Load (ETL) pipeline for health data extraction from HL7 CDA documents in Estonia for research purposes.

METHODS

We developed a repeatable ETL pipeline to facilitate the extraction, cleaning, and restructuring of health data from CDA documents to OMOP CDM, ensuring a high-quality and structured data format. This pipeline was designed to adapt to continuously updated data exchange format changes and handle various CDA document subsets for different scientific studies.

RESULTS

We demonstrated via selected use cases that our pipeline successfully transformed a significant portion of diagnosis codes, body weight and eGFR measurements, and PAP test results from CDA documents into OMOP CDM, showing the ease of extracting structured data. However, challenges such as harmonising diverse coding systems and extracting lab results from free-text sections were encountered. The iterative development of the pipeline facilitated swift error detection and correction, enhancing the process's efficiency.

CONCLUSION

After a decade of focused work, our research has led to the development of an ETL pipeline that effectively transforms HL7 CDA documents into OMOP CDM in Estonia, addressing key data extraction and transformation challenges. The pipeline's repeatability and adaptability to various data subsets make it a valuable resource for researchers dealing with health data. While tested on Estonian data, the principles outlined are broadly applicable, potentially aiding in handling health data standards that vary by country. Despite newer health data standards emerging, the relevance of CDA for retrospective health studies ensures the continuing importance of this work.

Big data research is everyone's research-Making epilepsy data science accessible to the global community: Report of the ILAE big data commission

Epilepsy care generates multiple sources of high-dimensional data, including clinical, imaging, electroencephalographic, genomic, and neuropsychological information, that are collected routinely to establish the diagnosis and guide management. Thanks to high-performance computing, sophisticated graphics processing units, and advanced analytics, we are now on the cusp of being able to use these data to significantly improve individualized care for people with epilepsy. Despite this, many clinicians, health care providers, and people with epilepsy are apprehensive about implementing Big Data and accompanying technologies such as artificial intelligence (AI). Practical, ethical, privacy, and climate issues represent real and enduring concerns that have yet to be completely resolved. Similarly, Big Data and AI-related biases have the potential to exacerbate local and global disparities. These are highly germane concerns to the field of epilepsy, given its high burden in developing nations and areas of socioeconomic deprivation. This educational paper from the International League Against Epilepsy's (ILAE) Big Data Commission aims to help clinicians caring for people with epilepsy become familiar with how Big Data is collected and processed, how they are applied to studies using AI, and outline the immense potential positive impact Big Data can have on diagnosis and management.

Augmenting the Hospital Score with social risk factors to improve prediction for 30-day readmission following acute myocardial infarction

Background

Hospital Score is a well-known and validated tool for predicting readmission risk among diverse patient populations. Integrating social risk factors using natural language processing with the Hospital Score may improve its ability to predict 30-day readmissions following an acute myocardial infarction.

Methods

A retrospective cohort included patients hospitalized at Vanderbilt University Medical Center between January 1, 2007, and December 31, 2016, with a primary index diagnosis of acute myocardial infarction, who were discharged alive. To supplement ascertainment of 30-day readmissions, data were linked to Center for Medicare & Medicaid Services (CMS) administrative data. Clinical notes from the cohort were extracted, and a natural language processing model was deployed, counting mentions of eight social risk factors. A logistic regression prediction model was run using the Hospital Score composite, its component variables, and the natural language processing-derived social risk factors. ROC comparison analysis was performed.

Results

The cohort included 6,165 unique patients, where 4,137 (67.1%) were male, 1,020 (16.5%) were Black or other people of color, the average age was 67 years (SD: 13), and the 30-day hospital readmission rate was 15.1% (N=934). The final test-set AUROCs were between 0.635 and 0.669. The model containing the Hospital Score component variables and the natural language processing-derived social risk factors obtained the highest AUROC.

Discussion

Social risk factors extracted using natural language processing improved model performance when added to the Hospital Score composite. Clinicians and health systems should consider incorporating social risk factors when using the Hospital Score composite to evaluate risk for readmission among patients hospitalized for acute myocardial infarction.

The arisal of data spaces: why I am excited and worried

This paper explores the significant role of real-world data (RWD) in advancing our understanding and management of Multiple Sclerosis (MS). RWD has proven invaluable in MS research and care, offering insights from larger and diverse patient populations. A key focus of the paper is the European Health Data Space (EHDS), a significant development that promises to change how healthcare data is managed across Europe. This initiative is particularly relevant to the MS community. The paper highlights various data initiatives, discussing their importance for those affected by MS. Despite the potential benefits, there are challenges and concerns, especially about ensuring that the growth of various data platforms remains beneficial for MS patients. The paper suggests practical actions for the global MS community to consider, aimed at optimizing the use of RWD. The emphasis of this discussion is on the secondary use of health data, particularly in the European context. The content is based on the author's own experiences and interpretations, offering a personal yet informed view on using RWD to improve MS research and patient care.

Trends in Antidiabetic Drug Use and Safety of Metformin in Diabetic Patients with Varying Degrees of Chronic Kidney Disease from 2010 to 2021 in Korea: Retrospective Cohort Study Using the Common Data Model

BACKGROUND/OBJECTIVES

This study aimed to investigate trends in antidiabetic drug use and assess the risk of metformin-associated lactic acidosis (MALA) in patients with chronic kidney disease (CKD).

METHODS

A retrospective observational analysis based on the common data model was conducted using electronic medical records from 2010 to 2021. The patients included were aged ≥18, diagnosed with CKD and type 2 diabetes, and had received antidiabetic medications for ≥30 days. MALA was defined as pH ≤ 7.35 and arterial lactate ≥4 mmol/L.

RESULTS

A total of 8318 patients were included, with 6185 in CKD stages 1-2 and 2133 in stages 3a-5. Metformin monotherapy was the most prescribed regimen, except in stage 5 CKD. As CKD progressed, metformin use significantly declined; insulin and meglitinides were most frequently prescribed in end-stage renal disease. Over the study period, the use of SGLT2 inhibitors (13.3%) and DPP-4 inhibitors (24.5%) increased significantly, while sulfonylurea use decreased (p < 0.05). Metformin use remained stable in earlier CKD stages but significantly decreased in stage 3b or worse. The incidence rate (IR) of MALA was 1.22 per 1000 patient-years, with a significantly increased IR in stage 4 or worse CKD (p < 0.001).

CONCLUSIONS

Metformin was the most prescribed antidiabetic drug in CKD patients in Korea with a low risk of MALA. Antidiabetic drug use patterns varied across CKD stages, with a notable decline in metformin use in advanced CKD and a rise in SGLT2 inhibitor prescriptions, underscoring the need for further optimized therapy.

Automating surgical procedure extraction for society of surgeons adult cardiac surgery registry using pretrained language models

Objective

Surgical registries play a crucial role in clinical knowledge discovery, hospital quality assurance, and quality improvement. However, maintaining a surgical registry requires significant monetary and human resources given the wide gamut of information abstracted from medical records ranging from patient co-morbidities to procedural details to post-operative outcomes. Although natural language processing (NLP) methods such as pretrained language models (PLMs) have promised automation of this process, there are yet substantial barriers to implementation. In particular, constant shifts in both underlying data and required registry content are hurdles to the application of NLP technologies.

Materials and Methods

In our work, we evaluate the application of PLMs for automating the population of the Society of Thoracic Surgeons (STSs) adult cardiac surgery registry (ACS) procedural elements, for which we term Cardiovascular Surgery Bidirectional Encoder Representations from Transformers (CS-BERT). CS-BERT was validated across multiple satellite sites and versions of the STS-ACS registry.

Results

CS-BERT performed well (F1 score of 0.8417 ± 0.1838) in common cardiac surgery procedures compared to models based on diagnosis codes (F1 score of 0.6130 ± 0.0010). The model also generalized well to satellite sites and across different versions of the STS-ACS registry.

Discussion and Conclusions

This study provides evidence that PLMs can be used to extract the more common cardiac surgery procedure variables in the STS-ACS registry, potentially reducing need for expensive human annotation and wide scale dissemination. Further research is needed for rare procedural variables which suffer from both lack of data and variable documentation quality.

Genetics and precision genomics approaches to pulmonary hypertension

Considerable progress has been made in the genomics of pulmonary arterial hypertension (PAH) since the 6th World Symposium on Pulmonary Hypertension, with the identification of rare variants in several novel genes, as well as common variants that confer a modest increase in PAH risk. Gene and variant curation by an expert panel now provides a robust framework for knowing which genes to test and how to interpret variants in clinical practice. We recommend that genetic testing be offered to specific subgroups of symptomatic patients with PAH, and to children with certain types of group 3 pulmonary hypertension (PH). Testing of asymptomatic family members and the use of genetics in reproductive decision-making require the involvement of genetics experts. Large cohorts of PAH patients with biospecimens now exist and extension to non-group 1 PH has begun. However, these cohorts are largely of European origin; greater diversity will be essential to characterise the full extent of genomic variation contributing to PH risk and treatment responses. Other types of omics data are also being incorporated. Furthermore, to advance gene- and pathway-specific care and targeted therapies, gene-specific registries will be essential to support patients and their families and to lay the foundation for genetically informed clinical trials. This will require international outreach and collaboration between patients/families, clinicians and researchers. Ultimately, harmonisation of patient-derived biospecimens, clinical and omic information, and analytic approaches will advance the field.

Implementation of the Observational Medical Outcomes Partnership Model in Electronic Medical Record Systems: Evaluation Study Using Factor Analysis and Decision-Making Trial and Evaluation Laboratory-Best-Worst Methods

BACKGROUND

Electronic medical record (EMR) systems are essential in health care for collecting and storing patient medical data. They provide critical information to doctors and caregivers, facilitating improved decision-making and patient care. Despite their significance, optimizing EMR systems is crucial for enhancing health care quality. Implementing the Observational Medical Outcomes Partnership (OMOP) shared data model represents a promising approach to improve EMR performance and overall health care outcomes.

OBJECTIVE

This study aims to evaluate the effects of implementing the OMOP shared data model in EMR systems and to assess its impact on enhancing health care quality.

METHODS

In this study, 3 distinct methodologies are used to explore various aspects of health care information systems. First, factor analysis is utilized to investigate the correlations between EMR systems and attitudes toward OMOP. Second, the best-worst method (BWM) is applied to determine the weights of criteria and subcriteria. Lastly, the decision-making trial and evaluation laboratory technique is used to illustrate the interactions and interdependencies among the identified criteria.

RESULTS

In this research, we evaluated the AliHealth EMR system by surveying 98 users and practitioners to assess its effectiveness and user satisfaction. The study reveals that among all components, "EMR resolution" holds the highest importance with a weight of 0.31007783, highlighting its significant role in the evaluation. Conversely, "EMR ease of use" has the lowest weight of 0.1860467, indicating that stakeholders prioritize the resolution aspect over ease of use in their assessment of EMR systems.

CONCLUSIONS

The findings highlight that stakeholders prioritize certain aspects of EMR systems, with "EMR resolution" being the most valued component.

The reuse of electronic health records information models in the oncology domain: Studies with the bioframe framework

OBJECTIVE

The reuse of Electronic Health Records (EHR) information models (e.g., templates and archetypes) may bring various benefits, including higher standardization, integration, interoperability, increased productivity in developing EHR systems, and unlock potential Artificial Intelligence applications built on top of medical records. The literature presents recent advances in standards for modeling EHR, in Knowledge Organization Systems (KOS) and EHR data reuse. However, methods, development processes, and frameworks to improve the reuse of EHR information models are still scarce. This study proposes a software engineering framework, named BioFrame, and analyzes how the reuse of EHR information models can be improved during the development of EHR systems.

METHODS

EHR standards and KOS, including ontologies, identified from systematic reviews were considered in developing the BioFrame framework. We used the structure of the OpenEHR to model templates and archetypes, as well as its relationship to international KOS used in the oncology domain. Our framework was applied in the context of pediatric oncology. Three data entry forms concerning nutrition and one utilized during the first pediatric oncology consultations were analyzed to measure the reuse of information models.

RESULTS

There was an increase in the adherence rate to international KOS of 18% to the original forms. There was an increase in the concepts reused in all 12 scenarios analyzed, with an average reuse of 6.55% in the original forms compared to 17.1% using BioFrame, resulting in significant differences.

CONCLUSIONS

Our results point to higher reuse rates achieved due to an engineering process that provided greater adherence to EHR standards combined with semantic artifacts. This reveals the potential to develop new methods and frameworks aimed at EHR information model reuse. Additional research is needed to evaluate the impacts of the reuse of the EHR information model on interoperability, EHR data reuse, and data quality and assess the proposed framework in other health domains.

Computational Approaches to Drug Repurposing: Methods, Challenges, and Opportunities

Drug repurposing refers to the inference of therapeutic relationships between a clinical indication and existing compounds. As an emerging paradigm in drug development, drug repurposing enables more efficient treatment of rare diseases, stratified patient populations, and urgent threats to public health. However, prioritizing well-suited drug candidates from among a nearly infinite number of repurposing options continues to represent a significant challenge in drug development. Over the past decade, advances in genomic profiling, database curation, and machine learning techniques have enabled more accurate identification of drug repurposing candidates for subsequent clinical evaluation. This review outlines the major methodologic classes that these approaches comprise, which rely on (a) protein structure, (b) genomic signatures, (c) biological networks, and (d) real-world clinical data. We propose that realizing the full impact of drug repurposing methodologies requires a multidisciplinary understanding of each method's advantages and limitations with respect to clinical practice.

Data harmonization and federated learning for multi-cohort dementia research using the OMOP common data model: A Netherlands consortium of dementia cohorts case study

BACKGROUND

Establishing collaborations between cohort studies has been fundamental for progress in health research. However, such collaborations are hampered by heterogeneous data representations across cohorts and legal constraints to data sharing. The first arises from a lack of consensus in standards of data collection and representation across cohort studies and is usually tackled by applying data harmonization processes. The second is increasingly important due to raised awareness for privacy protection and stricter regulations, such as the GDPR. Federated learning has emerged as a privacy-preserving alternative to transferring data between institutions through analyzing data in a decentralized manner.

METHODS

In this study, we set up a federated learning infrastructure for a consortium of nine Dutch cohorts with appropriate data available to the etiology of dementia, including an extract, transform, and load (ETL) pipeline for data harmonization. Additionally, we assessed the challenges of transforming and standardizing cohort data using the Observational Medical Outcomes Partnership (OMOP) common data model (CDM) and evaluated our tool in one of the cohorts employing federated algorithms.

RESULTS

We successfully applied our ETL tool and observed a complete coverage of the cohorts' data by the OMOP CDM. The OMOP CDM facilitated the data representation and standardization, but we identified limitations for cohort-specific data fields and in the scope of the vocabularies available. Specific challenges arise in a multi-cohort federated collaboration due to technical constraints in local environments, data heterogeneity, and lack of direct access to the data.

CONCLUSION

In this article, we describe the solutions to these challenges and limitations encountered in our study. Our study shows the potential of federated learning as a privacy-preserving solution for multi-cohort studies that enhance reproducibility and reuse of both data and analyses.

[An integrated system of neurovascular and mental disease registries]

A nemzetközi regiszterépítési gyakorlat fejlődését is figyelembe vevő, 18 kiemelt hazai regiszter működését rendező 2018. évi jogi szabályozás eredményeképpen szélesebb körben rendezetté vált a személyhez kötött egészségügyi adatok kezelése, megindulhatott a működtető környezet korszerű alapokra helyezése, és megújulhatott az adatok feldolgozási és elemzési folyamata. A személyes adatok kezelésére vonatkozó felhatalmazás alapján technikailag lehetségessé vált a különböző adatforrásokból érkező adatok összekapcsolása, s ezt kiaknázva a Nemzeti Stroke Regiszter és a Nemzeti Affektív Betegségek Regisztere esetén egy összetett regiszterrendszer jött létre. A regiszterrendszer adatokat tud fogadni az ágazat központi adatrendszereiből, a kórházi informatikai rendszerből és webes űrlapokon keresztül közvetlenül a betegellátóktól. Az adatokat egy többszintű, automatizált feldolgozási folyamatokkal támogatott adatbázisrendszer kezeli, amelynek működését irányítópult és jelentéskészítő funkciók is segítik. A feldolgozás magasabb rétegeiben az elemi adatok OMOP-alapú adatmodellt alkotnak, illetve az események láncokká állnak össze, lehetővé téve a komplex betegutak elemzését. A rendszer jelenleg több mint 50 millió ellátási eseményt, közel 100 millió dokumentumot és több mint 200 millió receptet kezel, amely nemzetközi szinten is kiemelkedő adatvagyont képez. Az adatbiztonságot összetett védelmi intézkedések szolgálják, beleértve az adatok álnevesítését és a kutatói adatpiacok szeparációját is. Összetettségüknek, adatmélységüknek és biztonságuknak köszönhetően ezek a regiszterek számtalan kutatásnak tudnak értékes adatforrást biztosítani. Orv Hetil. 2024; 165(24–25): 955–964.

Transforming a Large-Scale Prostate Cancer Outcomes Dataset to the OMOP Common Data Model-Experiences from a Scientific Data Holder's Perspective

To enhance international and joint research collaborations in prostate cancer research, data from different sources should use a common data model (CDM) that enables researchers to share their analysis scripts and merge results. The OMOP CDM maintained by OHDSI is such a data model developed for a federated data analysis with partners from different institutions that want to jointly investigate research questions using clinical care data. The German Cancer Society as the scientific lead of the Prostate Cancer Outcomes (PCO) study gathers data from prostate cancer care including routine oncological care data and survey data (incl. patient-reported outcomes) and uses a common data specification (called OncoBox Research Prostate) for this purpose. To further enhance research collaborations outside the PCO study, the purpose of this article is to describe the process of transferring the PCO study data to the internationally well-established OMOP CDM. This process was carried out together with an IT company that specialised in supporting research institutions to transfer their data to OMOP CDM. Of n = 49,692 prostate cancer cases with 318 data fields each, n = 392 had to be excluded during the OMOPing process, and n = 247 of the data fields could be mapped to OMOP CDM. The resulting PostgreSQL database with OMOPed PCO study data is now ready to use within larger research collaborations such as the EU-funded EHDEN and OPTIMA consortium.

Scoping review of the recommendations and guidance for improving the quality of rare disease registries

BACKGROUND

Rare disease registries (RDRs) are valuable tools for improving clinical care and advancing research. However, they often vary qualitatively, structurally, and operationally in ways that can determine their potential utility as a source of evidence to support decision-making regarding the approval and funding of new treatments for rare diseases.

OBJECTIVES

The goal of this research project was to review the literature on rare disease registries and identify best practices to improve the quality of RDRs.

METHODS

In this scoping review, we searched MEDLINE and EMBASE as well as the websites of regulatory bodies and health technology assessment agencies from 2010 to April 2023 for literature offering guidance or recommendations to ensure, improve, or maintain quality RDRs.

RESULTS

The search yielded 1,175 unique references, of which 64 met the inclusion criteria. The characteristics of RDRs deemed to be relevant to their quality align with three main domains and several sub-domains considered to be best practices for quality RDRs: (1) governance (registry purpose and description; governance structure; stakeholder engagement; sustainability; ethics/legal/privacy; data governance; documentation; and training and support); (2) data (standardized disease classification; common data elements; data dictionary; data collection; data quality and assurance; and data analysis and reporting); and (3) information technology (IT) infrastructure (physical and virtual infrastructure; and software infrastructure guided by FAIR principles (Findability; Accessibility; Interoperability; and Reusability).

CONCLUSIONS

Although RDRs face numerous challenges due to their small and dispersed populations, RDRs can generate quality data to support healthcare decision-making through the use of standards and principles on strong governance, quality data practices, and IT infrastructure.

The OMOP common data model in Australian primary care data: Building a quality research ready harmonised dataset

BACKGROUND

The use of routinely collected health data for secondary research purposes is increasingly recognised as a methodology that advances medical research, improves patient outcomes, and guides policy. This secondary data, as found in electronic medical records (EMRs), can be optimised through conversion into a uniform data structure to enable analysis alongside other comparable health metric datasets. This can be achieved with the Observational Medical Outcomes Partnership Common Data Model (OMOP-CDM), which employs a standardised vocabulary to facilitate systematic analysis across various observational databases. The concept behind the OMOP-CDM is the conversion of data into a common format through the harmonisation of terminologies, vocabularies, and coding schemes within a unique repository. The OMOP model enhances research capacity through the development of shared analytic and prediction techniques; pharmacovigilance for the active surveillance of drug safety; and 'validation' analyses across multiple institutions across Australia, the United States, Europe, and the Asia Pacific. In this research, we aim to investigate the use of the open-source OMOP-CDM in the PATRON primary care data repository.

METHODS

We used standard structured query language (SQL) to construct, extract, transform, and load scripts to convert the data to the OMOP-CDM. The process of mapping distinct free-text terms extracted from various EMRs presented a substantial challenge, as many terms could not be automatically matched to standard vocabularies through direct text comparison. This resulted in a number of terms that required manual assignment. To address this issue, we implemented a strategy where our clinical mappers were instructed to focus only on terms that appeared with sufficient frequency. We established a specific threshold value for each domain, ensuring that more than 95% of all records were linked to an approved vocabulary like SNOMED once appropriate mapping was completed. To assess the data quality of the resultant OMOP dataset we utilised the OHDSI Data Quality Dashboard (DQD) to evaluate the plausibility, conformity, and comprehensiveness of the data in the PATRON repository according to the Kahn framework.

RESULTS

Across three primary care EMR systems we converted data on 2.03 million active patients to version 5.4 of the OMOP common data model. The DQD assessment involved a total of 3,570 individual evaluations. Each evaluation compared the outcome against a predefined threshold. A 'FAIL' occurred when the percentage of non-compliant rows exceeded the specified threshold value. In this assessment of the primary care OMOP database described here, we achieved an overall pass rate of 97%.

CONCLUSION

The OMOP CDM's widespread international use, support, and training provides a well-established pathway for data standardisation in collaborative research. Its compatibility allows the sharing of analysis packages across local and international research groups, which facilitates rapid and reproducible data comparisons. A suite of open-source tools, including the OHDSI Data Quality Dashboard (Version 1.4.1), supports the model. Its simplicity and standards-based approach facilitates adoption and integration into existing data processes.

Building ontology-based temporal databases for data reuse: An applied example on hospital organizational structures

Keeping track of data semantics and data changes in the databases is essential to support retrospective studies and the reproducibility of longitudinal clinical analysis by preventing false conclusions from being drawn from outdated data. A knowledge model combined with a temporal model plays an essential role in organizing the data and improving query expressiveness across time and multiple institutions. This paper presents a modelling framework for temporal relational databases using an ontology to derive a shareable and interoperable data model. The framework is based on: OntoRela an ontology-driven database modelling approach and Unified Historicization Framework a temporal database modelling approach. The method was applied to hospital organizational structures to show the impact of tracking organizational changes on data quality assessment, healthcare activities and data access rights. The paper demonstrated the usefulness of an ontology to provide a formal, interoperable, and reusable definition of entities and their relationships, as well as the adequacy of the temporal database to store, trace, and query data over time.

Proceedings from the inaugural Artificial Intelligence in Primary Immune Deficiencies (AIPID) conference

Here, we summarize the proceedings of the inaugural Artificial Intelligence in Primary Immune Deficiencies conference, during which experts and advocates gathered to advance research into the applications of artificial intelligence (AI), machine learning, and other computational tools in the diagnosis and management of inborn errors of immunity (IEIs). The conference focused on the key themes of expediting IEI diagnoses, challenges in data collection, roles of natural language processing and large language models in interpreting electronic health records, and ethical considerations in implementation. Innovative AI-based tools trained on electronic health records and claims databases have discovered new patterns of warning signs for IEIs, facilitating faster diagnoses and enhancing patient outcomes. Challenges in training AIs persist on account of data limitations, especially in cases of rare diseases, overlapping phenotypes, and biases inherent in current data sets. Furthermore, experts highlighted the significance of ethical considerations, data protection, and the necessity for open science principles. The conference delved into regulatory frameworks, equity in access, and the imperative for collaborative efforts to overcome these obstacles and harness the transformative potential of AI. Concerted efforts to successfully integrate AI into daily clinical immunology practice are still needed.

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

BACKGROUND

To 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.

METHODS

For 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.

RESULTS

From 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.

CONCLUSIONS

The generic data harmonization process can be used as a step-by-step guide to assist other researchers in harmonizing source data in OMOP CDM.

Seamless EMR data access: Integrated governance, digital health and the OMOP-CDM

Objectives In this overview, we describe theObservational Medical Outcomes Partnership Common Data Model (OMOP-CDM), the established governance processes employed in EMR data repositories, and demonstrate how OMOP transformed data provides a lever for more efficient and secure access to electronic medical record (EMR) data by health service providers and researchers.Methods Through pseudonymisation and common data quality assessments, the OMOP-CDM provides a robust framework for converting complex EMR data into a standardised format. This allows for the creation of shared end-to-end analysis packages without the need for direct data exchange, thereby enhancing data security and privacy. By securely sharing de-identified and aggregated data and conducting analyses across multiple OMOP-converted databases, patient-level data is securely firewalled within its respective local site.Results By simplifying data management processes and governance, and through the promotion of interoperability, the OMOP-CDM supports a wide range of clinical, epidemiological, and translational research projects, as well as health service operational reporting.Discussion Adoption of the OMOP-CDM internationally and locally enables conversion of vast amounts of complex, and heterogeneous EMR data into a standardised structured data model, simplifies governance processes, and facilitates rapid repeatable cross-institution analysis through shared end-to-end analysis packages, without the sharing of data.Conclusion The adoption of the OMOP-CDM has the potential to transform health data analytics by providing a common platform for analysing EMR data across diverse healthcare settings.

A Federated Database for Obesity Research: An IMI-SOPHIA Study

Obesity is considered by many as a lifestyle choice rather than a chronic progressive disease. The Innovative Medicines Initiative (IMI) SOPHIA (Stratification of Obesity Phenotypes to Optimize Future Obesity Therapy) project is part of a momentum shift aiming to provide better tools for the stratification of people with obesity according to disease risk and treatment response. One of the challenges to achieving these goals is that many clinical cohorts are siloed, limiting the potential of combined data for biomarker discovery. In SOPHIA, we have addressed this challenge by setting up a federated database building on open-source DataSHIELD technology. The database currently federates 16 cohorts that are accessible via a central gateway. The database is multi-modal, including research studies, clinical trials, and routine health data, and is accessed using the R statistical programming environment where statistical and machine learning analyses can be performed at a distance without any disclosure of patient-level data. We demonstrate the use of the database by providing a proof-of-concept analysis, performing a federated linear model of BMI and systolic blood pressure, pooling all data from 16 studies virtually without any analyst seeing individual patient-level data. This analysis provided similar point estimates compared to a meta-analysis of the 16 individual studies. Our approach provides a benchmark for reproducible, safe federated analyses across multiple study types provided by multiple stakeholders.

Using A Standardized Nomenclature to Semantically Map Oncology-Related Concepts from Common Data Models to a Pediatric Cancer Data Model

The Pediatric Cancer Data Commons (PCDC) comprises an international community whose ironclad commitment to data sharing is combatting pediatric cancer in an unprecedented way. The byproduct of their data sharing efforts is a gold-standard consensus data model covering many types of pediatric cancer. This article describes an effort to utilize SSSOM, an emerging specification for semantically-rich data mappings, to provide a "hub and spoke" model of mappings from several common data models (CDMs) to the PCDC data model. This provides important contributions to the research community, including: 1) a clear view of the current coverage of these CDMs in the domain of pediatric oncology, and 2) a demonstration of creating standardized mappings. These mappings can allow downstream crosswalk for data transformation and enhance data sharing. This can guide those who currently create and maintain brittle ad hoc data mappings in order to utilize the growing volume of viable research data.

European Health Data & Evidence Network-learnings from building out a standardized international health data network

OBJECTIVE

Health data standardized to a common data model (CDM) simplifies and facilitates research. This study examines the factors that make standardizing observational health data to the Observational Medical Outcomes Partnership (OMOP) CDM successful.

MATERIALS AND METHODS

Twenty-five data partners (DPs) from 11 countries received funding from the European Health Data Evidence Network (EHDEN) to standardize their data. Three surveys, DataQualityDashboard results, and statistics from the conversion process were analyzed qualitatively and quantitatively. Our measures of success were the total number of days to transform source data into the OMOP CDM and participation in network research.

RESULTS

The health data converted to CDM represented more than 133 million patients. 100%, 88%, and 84% of DPs took Surveys 1, 2, and 3. The median duration of the 6 key extract, transform, and load (ETL) processes ranged from 4 to 115 days. Of the 25 DPs, 21 DPs were considered applicable for analysis of which 52% standardized their data on time, and 48% participated in an international collaborative study.

DISCUSSION

This study shows that the consistent workflow used by EHDEN proves appropriate to support the successful standardization of observational data across Europe. Over the 25 successful transformations, we confirmed that getting the right people for the ETL is critical and vocabulary mapping requires specific expertise and support of tools. Additionally, we learned that teams that proactively prepared for data governance issues were able to avoid considerable delays improving their ability to finish on time.

CONCLUSION

This study provides guidance for future DPs to standardize to the OMOP CDM and participate in distributed networks. We demonstrate that the Observational Health Data Sciences and Informatics community must continue to evaluate and provide guidance and support for what ultimately develops the backbone of how community members generate evidence.

Advancing Toward a Common Data Model in Ophthalmology: Gap Analysis of General Eye Examination Concepts to Standard Observational Medical Outcomes Partnership (OMOP) Concepts

Purpose

Evaluate the degree of concept coverage of the general eye examination in one widely used electronic health record (EHR) system using the Observational Health Data Sciences and Informatics Observational Medical Outcomes Partnership (OMOP) common data model (CDM).

Design

Study of data elements.

Participants

Not applicable.

Methods

Data elements (field names and predefined entry values) from the general eye examination in the Epic foundation system were mapped to OMOP concepts and analyzed. Each mapping was given a Health Level 7 equivalence designation-equal when the OMOP concept had the same meaning as the source EHR concept, wider when it was missing information, narrower when it was overly specific, and unmatched when there was no match. Initial mappings were reviewed by 2 graders. Intergrader agreement for equivalence designation was calculated using Cohen's kappa. Agreement on the mapped OMOP concept was calculated as a percentage of total mappable concepts. Discrepancies were discussed and a final consensus created. Quantitative analysis was performed on wider and unmatched concepts.

Main Outcome Measures

Gaps in OMOP concept coverage of EHR elements and intergrader agreement of mapped OMOP concepts.

Results

A total of 698 data elements (210 fields, 488 values) from the EHR were analyzed. The intergrader kappa on the equivalence designation was 0.88 (standard error 0.03, P < 0.001). There was a 96% agreement on the mapped OMOP concept. In the final consensus mapping, 25% (1% fields, 31% values) of the EHR to OMOP concept mappings were considered equal, 50% (27% fields, 60% values) wider, 4% (8% fields, 2% values) narrower, and 21% (52% fields, 8% values) unmatched. Of the wider mapped elements, 46% were missing the laterality specification, 24% had other missing attributes, and 30% had both issues. Wider and unmatched EHR elements could be found in all areas of the general eye examination.

Conclusions

Most data elements in the general eye examination could not be represented precisely using the OMOP CDM. Our work suggests multiple ways to improve the incorporation of important ophthalmology concepts in OMOP, including adding laterality to existing concepts. There exists a strong need to improve the coverage of ophthalmic concepts in source vocabularies so that the OMOP CDM can better accommodate vision research.

Financial Disclosures

Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Transforming Estonian health data to the Observational Medical Outcomes Partnership (OMOP) Common Data Model: lessons learned

Objective

To describe the reusable transformation process of electronic health records (EHR), claims, and prescriptions data into Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM), together with challenges faced and solutions implemented.

Materials and Methods

We used Estonian national health databases that store almost all residents' claims, prescriptions, and EHR records. To develop and demonstrate the transformation process of Estonian health data to OMOP CDM, we used a 10% random sample of the Estonian population (n = 150 824 patients) from 2012 to 2019 (MAITT dataset). For the sample, complete information from all 3 databases was converted to OMOP CDM version 5.3. The validation was performed using open-source tools.

Results

In total, we transformed over 100 million entries to standard concepts using standard OMOP vocabularies with the average mapping rate 95%. For conditions, observations, drugs, and measurements, the mapping rate was over 90%. In most cases, SNOMED Clinical Terms were used as the target vocabulary.

Discussion

During the transformation process, we encountered several challenges, which are described in detail with concrete examples and solutions.

Conclusion

For a representative 10% random sample, we successfully transferred complete records from 3 national health databases to OMOP CDM and created a reusable transformation process. Our work helps future researchers to transform linked databases into OMOP CDM more efficiently, ultimately leading to better real-world evidence.

Healthcare data quality assessment for improving the quality of the Korea Biobank Network

Numerous studies make extensive use of healthcare data, including human materials and clinical information, and acknowledge its significance. However, limitations in data collection methods can impact the quality of healthcare data obtained from multiple institutions. In order to secure high-quality data related to human materials, research focused on data quality is necessary. This study validated the quality of data collected in 2020 from 16 institutions constituting the Korea Biobank Network using 104 validation rules. The validation rules were developed based on the DQ4HEALTH model and were divided into four dimensions: completeness, validity, accuracy, and uniqueness. Korea Biobank Network collects and manages human materials and clinical information from multiple biobanks, and is in the process of developing a common data model for data integration. The results of the data quality verification revealed an error rate of 0.74%. Furthermore, an analysis of the data from each institution was performed to examine the relationship between the institution's characteristics and error count. The results from a chi-square test indicated that there was an independent correlation between each institution and its error count. To confirm this correlation between error counts and the characteristics of each institution, a correlation analysis was conducted. The results, shown in a graph, revealed the relationship between factors that had high correlation coefficients and the error count. The findings suggest that the data quality was impacted by biases in the evaluation system, including the institution's IT environment, infrastructure, and the number of collected samples. These results highlight the need to consider the scalability of research quality when evaluating clinical epidemiological information linked to human materials in future validation studies of data quality.

Assessing the Use of German Claims Data Vocabularies for Research in the Observational Medical Outcomes Partnership Common Data Model: Development and Evaluation Study

Background

National classifications and terminologies already routinely used for documentation within patient care settings enable the unambiguous representation of clinical information. However, the diversity of different vocabularies across health care institutions and countries is a barrier to achieving semantic interoperability and exchanging data across sites. The Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) enables the standardization of structure and medical terminology. It allows the mapping of national vocabularies into so-called standard concepts, representing normative expressions for international analyses and research. Within our project "Hybrid Quality Indicators Using Machine Learning Methods" (Hybrid-QI), we aim to harmonize source codes used in German claims data vocabularies that are currently unavailable in the OMOP CDM.

Objective

This study aims to increase the coverage of German vocabularies in the OMOP CDM. We aim to completely transform the source codes used in German claims data into the OMOP CDM without data loss and make German claims data usable for OMOP CDM-based research.

Methods

To prepare the missing German vocabularies for the OMOP CDM, we defined a vocabulary preparation approach consisting of the identification of all codes of the corresponding vocabularies, their assembly into machine-readable tables, and the translation of German designations into English. Furthermore, we used 2 proposed approaches for OMOP-compliant vocabulary preparation: the mapping to standard concepts using the Observational Health Data Sciences and Informatics (OHDSI) tool Usagi and the preparation of new 2-billion concepts (ie, concept_id >2 billion). Finally, we evaluated the prepared vocabularies regarding completeness and correctness using synthetic German claims data and calculated the coverage of German claims data vocabularies in the OMOP CDM.

Results

Our vocabulary preparation approach was able to map 3 missing German vocabularies to standard concepts and prepare 8 vocabularies as new 2-billion concepts. The completeness evaluation showed that the prepared vocabularies cover 44.3% (3288/7417) of the source codes contained in German claims data. The correctness evaluation revealed that the specified validity periods in the OMOP CDM are compliant for the majority (705,531/706,032, 99.9%) of source codes and associated dates in German claims data. The calculation of the vocabulary coverage showed a noticeable decrease of missing vocabularies from 55% (11/20) to 10% (2/20) due to our preparation approach.

Conclusions

By preparing 10 vocabularies, we showed that our approach is applicable to any type of vocabulary used in a source data set. The prepared vocabularies are currently limited to German vocabularies, which can only be used in national OMOP CDM research projects, because the mapping of new 2-billion concepts to standard concepts is missing. To participate in international OHDSI network studies with German claims data, future work is required to map the prepared 2-billion concepts to standard concepts.

Real-world evidence to advance knowledge in pulmonary hypertension: Status, challenges, and opportunities. A consensus statement from the Pulmonary Vascular Research Institute's Innovative Drug Development Initiative's Real-world Evidence Working Group

This manuscript on real-world evidence (RWE) in pulmonary hypertension (PH) incorporates the broad experience of members of the Pulmonary Vascular Research Institute's Innovative Drug Development Initiative Real-World Evidence Working Group. We aim to strengthen the research community's understanding of RWE in PH to facilitate clinical research advances and ultimately improve patient care. Herein, we review real-world data (RWD) sources, discuss challenges and opportunities when using RWD sources to study PH populations, and identify resources needed to support the generation of meaningful RWE for the global PH community.

Totality of evidence of the effectiveness of repurposed therapies for COVID-19: Can we use real-world studies alongside randomized controlled trials?

Rapid and robust strategies to evaluate the efficacy and effectiveness of novel and existing pharmacotherapeutic interventions (repurposed treatments) in future pandemics are required. Observational "real-world studies" (RWS) can report more quickly than randomized controlled trials (RCTs) and would have value were they to yield reliable results. Both RCTs and RWS were deployed during the coronavirus disease 2019 (COVID-19) pandemic. Comparing results between them offers a unique opportunity to determine the potential value and contribution of each. A learning review of these parallel evidence channels in COVID-19, based on quantitative modeling, can help improve speed and reliability in the evaluation of repurposed therapeutics in a future pandemic. Analysis of all-cause mortality data from 249 observational RWS and RCTs across eight treatment regimens for COVID-19 showed that RWS yield more heterogeneous results, and generally overestimate the effect size subsequently seen in RCTs. This is explained in part by a few study factors: the presence of RWS that are imbalanced for age, gender, and disease severity, and those reporting mortality at 2 weeks or less. Smaller studies of either type contributed negligibly. Analysis of evidence generated sequentially during the pandemic indicated that larger RCTs drive our ability to make conclusive decisions regarding clinical benefit of each treatment, with limited inference drawn from RWS. These results suggest that when evaluating therapies in future pandemics, (1) large RCTs, especially platform studies, be deployed early; (2) any RWS should be large and should have adequate matching of known confounders and long follow-up; (3) reporting standards and data standards for primary endpoints, explanatory factors, and key subgroups should be improved; in addition, (4) appropriate incentives should be in place to enable access to patient-level data; and (5) an overall aggregate view of all available results should be available at any given time.

Enabling data sharing and utilization for African population health data using OHDSI tools with an OMOP-common data model

The COVID-19 pandemic has spurred the use of AI and DS innovations in data collection and aggregation. Extensive data on many aspects of the COVID-19 has been collected and used to optimize public health response to the pandemic and to manage the recovery of patients in Sub-Saharan Africa. However, there is no standard mechanism for collecting, documenting and disseminating COVID-19 related data or metadata, which makes the use and reuse a challenge. INSPIRE utilizes the Observational Medical Outcomes Partnership (OMOP) as the Common Data Model (CDM) implemented in the cloud as a Platform as a Service (PaaS) for COVID-19 data. The INSPIRE PaaS for COVID-19 data leverages the cloud gateway for both individual research organizations and for data networks. Individual research institutions may choose to use the PaaS to access the FAIR data management, data analysis and data sharing capabilities which come with the OMOP CDM. Network data hubs may be interested in harmonizing data across localities using the CDM conditioned by the data ownership and data sharing agreements available under OMOP's federated model. The INSPIRE platform for evaluation of COVID-19 Harmonized data (PEACH) harmonizes data from Kenya and Malawi. Data sharing platforms must remain trusted digital spaces that protect human rights and foster citizens' participation is vital in an era where information overload from the internet exists. The channel for sharing data between localities is included in the PaaS and is based on data sharing agreements provided by the data producer. This allows the data producers to retain control over how their data are used, which can be further protected through the use of the federated CDM. Federated regional OMOP-CDM are based on the PaaS instances and analysis workbenches in INSPIRE-PEACH with harmonized analysis powered by the AI technologies in OMOP. These AI technologies can be used to discover and evaluate pathways that COVID-19 cohorts take through public health interventions and treatments. By using both the data mapping and terminology mapping, we construct ETLs that populate the data and/or metadata elements of the CDM, making the hub both a central model and a distributed model.

Assessing the FAIRness of databases on the EHDEN portal: A case study on two Dutch ICU databases

OBJECTIVE

To address the growing need for effective data reuse in health research, healthcare institutions need to make their data Findable, Accessible, Interoperable, and Reusable (FAIR). A prevailing method to model databases for interoperability is the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM), developed by the Observational Health Data Sciences and Informatics (OHDSI) initiative. A European repository for OMOP CDM-converted databases called the "European Health Data & Evidence Network (EHDEN) portal" was developed, aiming to make these databases Findable and Accessible. This paper aims to assess the FAIRness of databases on the EHDEN portal.

MATERIALS AND METHODS

Two researchers involved in the OMOP CDM conversion of separate Dutch Intensive Care Unit (ICU) research databases each manually assessed their own database using seventeen metrics. These were defined by the FAIRsFAIR project as a list of minimum requirements for a database to be FAIR. Each metric is given a score from zero to four based on how well the database adheres to the metric. The maximum score for each metric varies from one to four based on the importance of the metric.

RESULTS

Fourteen out of the seventeen metrics were unanimously rated: seven were rated the highest score, one was rated half of the highest score, and five were rated the lowest score. The remaining three metrics were assessed differently for the two use cases. The total scores achieved were 15.5 and 12 out of a maximum of 25.

CONCLUSION

The main omissions in supporting FAIRness were the lack of globally unique identifiers such as Uniform Resource Identifiers (URIs) in the OMOP CDM and the lack of metadata standardization and linkage in the EHDEN portal. By implementing these in future updates, the EHDEN portal can be more FAIR.