Observational Medical Outcomes Partnership Common Data Model Research Articles

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.

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.

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.

Patient-Centered Economic Burden of Exudative Age-Related Macular Degeneration: Retrospective Cohort Study.

Exudative age-related macular degeneration (AMD), one of the leading causes of blindness, requires expensive drugs such as anti-vascular endothelial growth factor (VEGF) agents. The long-term regular use of effective but expensive drugs causes an economic burden for patients with exudative AMD. However, there are no studies on the long-term patient-centered economic burden of exudative AMD after reimbursement of anti-VEGFs. This study aimed to evaluate the patient-centered economic burden of exudative AMD for 2 years, including nonreimbursement and out-of-pocket costs, compared with nonexudative AMD using the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). This retrospective cohort study was conducted using the OMOP CDM, which included 2,006,478 patients who visited Seoul National University Bundang Hospital from June 2003 to July 2019. We defined the exudative AMD group as patients aged >50 years with a diagnosis of exudative AMD and a prescription for anti-VEGFs or verteporfin. The control group was defined as patients aged >50 years without a diagnosis of exudative AMD or a prescription for anti-VEGFs or verteporfin. To adjust for selection bias, controls were matched by propensity scores using regularized logistic regression with a Laplace prior. We measured any medical cost occurring in the hospital as the economic burden of exudative AMD during a 2-year follow-up period using 4 categories: total medical cost, reimbursement cost, nonreimbursement cost, and out-of-pocket cost. To estimate the average cost by adjusting the confounding variable and overcoming the positive skewness of costs, we used an exponential conditional model with a generalized linear model. We identified 931 patients with exudative AMD and matched 783 (84.1%) with 2918 patients with nonexudative AMD. In the exponential conditional model, the total medical, reimbursement, nonreimbursement, and out-of-pocket incremental costs were estimated at US $3426, US $3130, US $366, and US $561, respectively, in the first year and US $1829, US $1461, US $373, and US $507, respectively, in the second year. All incremental costs in the exudative AMD group were 1.89 to 4.25 and 3.50 to 5.09 times higher in the first and second year, respectively, than those in the control group (P<.001 in all cases). Exudative AMD had a significantly greater economic impact (P<.001) for 2 years on reimbursement, nonreimbursement, and out-of-pocket costs than nonexudative AMD after adjusting for baseline demographic and clinical characteristics using the OMOP CDM. Although economic policies could relieve the economic burden of patients with exudative AMD over time, the out-of-pocket cost of exudative AMD was still higher than that of nonexudative AMD for 2 years. Our findings support the need for expanding reimbursement strategies for patients with exudative AMD given the significant economic burden faced by patients with incurable and fatal diseases both in South Korea and worldwide.

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

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. 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. 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. 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. 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.

IncidencePrevalence: An R package to calculate population-level incidence rates and prevalence using the OMOP common data model.

Real-world data (RWD) offers a valuable resource for generating population-level disease epidemiology metrics. We aimed to develop a well-tested and user-friendly R package to compute incidence rates and prevalence in data mapped to the observational medical outcomes partnership (OMOP) common data model (CDM). We created IncidencePrevalence, an R package to support the analysis of population-level incidence rates and point- and period-prevalence in OMOP-formatted data. On top of unit testing, we assessed the face validity of the package. To do so, we calculated incidence rates of COVID-19 using RWD from Spain (SIDIAP) and the United Kingdom (CPRD Aurum), and replicated two previously published studies using data from the Netherlands (IPCI) and the United Kingdom (CPRD Gold). We compared the obtained results to those previously published, and measured execution times by running a benchmark analysis across databases. IncidencePrevalence achieved high agreement to previously published data in CPRD Gold and IPCI, and showed good performance across databases. For COVID-19, incidence calculated by the package was similar to public data after the first-wave of the pandemic. For data mapped to the OMOP CDM, the IncidencePrevalence R package can support descriptive epidemiological research. It enables reliable estimation of incidence and prevalence from large real-world data sets. It represents a simple, but extendable, analytical framework to generate estimates in a reproducible and timely manner.

THU287 Comparison Of Renal Protective Effects Between SGLT2 Inhibitors And DPP4 Inhibitors In Real-World Clinical Practice

Abstract Disclosure: H. Park: None. S. Park: None. S. Kwon: None. H. Kim: None. D. Byun: None. Recent prospective randomized studies have shown that sodium-glucose cotransporter 2 (SGLT2) inhibitors had renal protective effects compared to placebo. In this study, we compared the renal composite outcomes between patients with diabetes treated with SGLT2 inhibitors and those treated with dipeptidyl peptidase 4 (DPP4) inhibitors using real-world clinical data. This retrospective observational study used the Observational Medical Outcomes Partnership Common Data Model (OMOP-CDM) database at four different university hospitals (Soonchunhyang university hospitals in Seoul, Bucheon, Chunan, and Gumi) in Korea. Subjects prescribed SGLT2 inhibitors or DPP4 inhibitors for at least 90 days were included in the SGLT2 inhibitor or DPP4 inhibitor group, respectively. Subjects prescribed GLP-1 receptor agonist or insulin were excluded in both groups. Renal composite outcomes included a 30% decline in estimated glomerular filtration rate (eGFR) compared to baseline or creatinine doubling or dialysis or death from any cause. After propensity score matching, clinical characteristics in each group at each hospital were well balanced at baseline. Our results from hospitals in Seoul, Bucheon, and Gumi have shown that SGLT2 inhibitor decreased renal composite outcomes compared to DPP4 inhibitor (hazard ratio (HR) 0.644, p=0.020; HR 0.560, p&amp;lt;0.001; HR 0.657, p=0.010, respectively). Furthermore, when all the data were combined, renal composite outcomes were significantly lower in the SGLT2 inhibitor group compared to the DPP4 inhibitor group (HR 0.659, p&amp;lt;0.001). In conclusion, SGLT2 inhibitors effectively reduce renal composite outcomes compared to DPP4 inhibitors in real-world clinical practice. Presentation: Thursday, June 15, 2023

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

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. 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 = 150824 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. 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. During the transformation process, we encountered several challenges, which are described in detail with concrete examples and solutions. 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.

Evaluation of OMOP CDM, i2b2 and ICGC ARGO for supporting data harmonization in a breast cancer use case of a multicentric European AI project

ObjectiveObservational research in cancer poses great challenges regarding adequate data sharing and consolidation based on a homogeneous data semantic base. Common Data Models (CDMs) can help consolidate health data repositories from different institutions minimizing loss of meaning by organizing data into a standard structure. This study aims to evaluate the performance of the Observational Medical Outcomes Partnership (OMOP) CDM, Informatics for Integrating Biology & the Bedside (i2b2) and International Cancer Genome Consortium, Accelerating Research in Genomic Oncology (ICGC ARGO) for representing non-imaging data in a breast cancer use case of EuCanImage. MethodsWe used ontologies to represent metamodels of OMOP, i2b2, and ICGC ARGO and variables used in a cancer use case of a European AI project. We selected four evaluation criteria for the CDMs adapted from previous research: content coverage, simplicity, integration, implementability. Resultsi2b2 and OMOP exhibited higher element completeness (100% each) than ICGC ARGO (58.1%), while the three achieved 100% domain completeness. ICGC ARGO normalizes only one of our variables with a standard terminology, while i2b2 and OMOP use standardized vocabularies for all of them. In terms of simplicity, ICGC ARGO and i2b2 proved to be simpler both in terms of ontological model (276 and 175 elements, respectively) and in the queries (7 and 20 lines of code, respectively), while OMOP required a much more complex ontological model (615 elements) and queries similar to those of i2b2 (20 lines). Regarding implementability, OMOP had the highest number of mentions in articles in PubMed (130) and Google Scholar (1,810), ICGC ARGO had the highest number of updates to the CDM since 2020 (4), and i2b2 is the model with more tools specifically developed for the CDM (26). ConclusionICGC ARGO proved to be rigid and very limited in the representation of oncologic concepts, while i2b2 and OMOP showed a very good performance. i2b2′s lack of a common dictionary hinders its scalability, requiring sites that will share data to explicitly define a conceptual framework, and suggesting that OMOP and its Oncology extension could be the more suitable choice. Future research employing these CDMs with actual datasets is needed.

Design and Implementation of an ETL-Process to Transfer Wound-Related Data into a Standardized Common Data Model.

For observational studies, which are relevant especially for chronic conditions like chronic wounds, the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) offers a standardized database schema. In this study an ETL process for the transition of wound related data was developed. After understanding the data in general and mapping the relevant codes to concepts available in OMOP, the ETL process was implemented. In a first step, a generic algorithm to convert data to a csv format was implemented in Java. The resulting csv file was then processed within KNIME to be loaded into an OMOP CDM conformant database. During the whole ETL process, HL7 FHIR CodeSystem and ConceptMap resources were used for coding and mapping. First clinical test cases to retrieve data were successfully processed as an example to demonstrate the feasibility and usefulness. They concerned wound size at the first visit and the main issues of patients in the wound quality of life questionnaire (n = 24). In general, the ETL process worked well, yet some challenges arose, like post coordinated SNOMED codes or conditions, which might occur more than once.

MI-Common Data Model: Extending Observational Medical Outcomes Partnership-Common Data Model (OMOP-CDM) for Registering Medical Imaging Metadata and Subsequent Curation Processes

PURPOSE The explosion of big data and artificial intelligence has rapidly increased the need for integrated, homogenized, and harmonized health data. Many common data models (CDMs) and standard vocabularies have appeared in an attempt to offer harmonized access to the available information, with Observational Medical Outcomes Partnership (OMOP)-CDM being one of the most prominent ones, allowing the standardization and harmonization of health care information. However, despite its flexibility, still capturing imaging metadata along with the corresponding clinical data continues to pose a challenge. This challenge arises from the absence of a comprehensive standard representation for image-related information and subsequent image curation processes and their interlinkage with the respective clinical information. Successful resolution of this challenge holds the potential to enable imaging and clinical data to become harmonized, quality-checked, annotated, and ready to be used in conjunction, in the development of artificial intelligence models and other data-dependent use cases. METHODS To address this challenge, we introduce medical imaging (MI)-CDM—an extension of the OMOP-CDM specifically designed for registering medical imaging data and curation-related processes. Our modeling choices were the result of iterative numerous discussions among clinical and AI experts to enable the integration of imaging and clinical data in the context of the ProCAncer-I project, for answering a set of clinical questions across the prostate cancer's continuum. RESULTS Our MI-CDM extension has been successfully implemented for the use case of prostate cancer for integrating imaging and curation metadata along with clinical information by using the OMOP-CDM and its oncology extension. CONCLUSION By using our proposed terminologies and standardized attributes, we demonstrate how diverse imaging modalities can be seamlessly integrated in the future.

Transforming the Information System for Research in Primary Care (SIDIAP) in Catalonia to the OMOP Common Data Model and Its Use for COVID-19 Research.

The primary aim of this work was to convert the Information System for Research in Primary Care (SIDIAP) from Catalonia, Spain, to the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). Our second aim was to provide a descriptive analysis of COVID-19-related outcomes among the general population. We mapped patient-level data from SIDIAP to the OMOP CDM and we performed more than 3,400 data quality checks to assess its readiness for research. We established a general population cohort as of the 1st March 2020 and identified outpatient COVID-19 diagnoses or tested positive for, hospitalised with, admitted to intensive care units (ICU) with, died with, or vaccinated against COVID-19 up to 30th June 2022. After verifying the high quality of the transformed dataset, we included 5,870,274 individuals in the general population cohort. Of those, 604,472 had either an outpatient COVID-19 diagnosis or positive test result, 58,991 had a hospitalisation, 5,642 had an ICU admission, and 11,233 died with COVID-19. A total of 4,584,515 received a COVID-19 vaccine. People who were hospitalised or died were more commonly older, male, and with more comorbidities. Those admitted to ICU with COVID-19 were generally younger and more often male than those hospitalised and those who died. We successfully transformed SIDIAP to the OMOP CDM. From this dataset, a general population cohort of 5.9 million individuals was identified and their COVID-19-related outcomes over time were described. The transformed SIDIAP database is a valuable resource that can enable distributed network research in COVID-19 and beyond.

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

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). Study of data elements. Not applicable. 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. Gaps in OMOP concept coverage of EHR elements and intergrader agreement of mapped OMOP concepts. 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. 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. Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

An Extract-Transform-Load Process Design for the Incremental Loading of German Real-World Data Based on FHIR and OMOP CDM: Algorithm Development and Validation.

In the Medical Informatics in Research and Care in University Medicine (MIRACUM) consortium, an IT-based clinical trial recruitment support system was developed based on the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). Currently, OMOP CDM is populated with German Fast Healthcare Interoperability Resources (FHIR) using an Extract-Transform-Load (ETL) process, which was designed as a bulk load. However, the computational effort that comes with an everyday full load is not efficient for daily recruitment. The aim of this study is to extend our existing ETL process with the option of incremental loading to efficiently support daily updated data. Based on our existing bulk ETL process, we performed an analysis to determine the requirements of incremental loading. Furthermore, a literature review was conducted to identify adaptable approaches. Based on this, we implemented three methods to integrate incremental loading into our ETL process. Lastly, a test suite was defined to evaluate the incremental loading for data correctness and performance compared to bulk loading. The resulting ETL process supports bulk and incremental loading. Performance tests show that the incremental load took 87.5% less execution time than the bulk load (2.12 min compared to 17.07 min) related to changes of 1 day, while no data differences occurred in OMOP CDM. Since incremental loading is more efficient than a daily bulk load and both loading options result in the same amount of data, we recommend using bulk load for an initial load and switching to incremental load for daily updates. The resulting incremental ETL logic can be applied internationally since it is not restricted to German FHIR profiles.

Mapping the Oncological Basis Dataset to the Standardized Vocabularies of a Common Data Model: A Feasibility Study.

In their joint effort against cancer, all involved parties within the German healthcare system are obligated to report diagnostics, treatments, progression, and follow-up information for tumor patients to the respective cancer registries. Given the federal structure of Germany, the oncological basis dataset (oBDS) operates as the legally required national standard for oncological reporting. Unfortunately, the usage of various documentation software solutions leads to semantic and technical heterogeneity of the data, complicating the establishment of research networks and collective data analysis. Within this feasibility study, we evaluated the transferability of all oBDS characteristics to the standardized vocabularies, a metadata repository of the observational medical outcomes partnership (OMOP) common data model (CDM). A total of 17,844 oBDS expressions were mapped automatically or manually to standardized concepts of the OMOP CDM. In a second step, we converted real patient data retrieved from the Hamburg Cancer Registry to the new terminologies. Given our pipeline, we transformed 1773.373 cancer-related data elements to the OMOP CDM. The mapping of the oBDS to the standardized vocabularies of the OMOP CDM promotes the semantic interoperability of oncological data in Germany. Moreover, it allows the participation in network studies of the observational health data sciences and informatics under the usage of federated analysis beyond the level of individual countries.

Eos and OMOCL: Towards a seamless integration of openEHR records into the OMOP Common Data Model

Background:The reuse of data from electronic health records (EHRs) for research purposes promises to improve the data foundation for clinical trials and may even support to enable them. Nevertheless, EHRs are characterized by both, heterogeneous structure and semantics. To standardize this data for research, the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) standard has recently seen an increase in use. However, the conversion of these EHRs into the OMOP CDM requires complex and resource intensive Extract Transform and Load (ETL) processes. This hampers the reuse of clinical data for research. To solve the issues of heterogeneity of EHRs and the lack of semantic precision on the care site, the openEHR standard has recently seen wider adoption. A standardized process to integrate openEHR records into the CDM potentially lowers the barriers of making EHRs accessible for research. Yet, a comprehensive approach about the integration of openEHR records into the OMOP CDM has not yet been made. Methods:We analyzed both standards and compared their models to identify possible mappings. Based on this, we defined the necessary processes to transform openEHR records into CDM tables. We also discuss the limitation of openEHR with its unspecific demographics model and propose two possible solutions. Results:We developed the OMOP Conversion Language (OMOCL) which enabled us to define a declarative openEHR archetype-to-CDM mapping language. Using OMOCL, it was possible to define a set of mappings. As a proof-of-concept, we implemented the Eos tool, which uses the OMOCL-files to successfully automatize the ETL from real-world and sample EHRs into the OMOP CDM. Discussion:Both Eos and OMOCL provide a way to define generic mappings for an integration of openEHR records into OMOP. Thus, it represents a significant step towards achieving interoperability between the clinical and the research data domains. However, the transformation of openEHR data into the less expressive OMOP CDM leads to a loss of semantics.

Association between dyslipidemia and asthma in children: a systematic review and multicenter cohort study using a common data model.

The association between dyslipidemia and asthma in children remains unclear. This study investigated the association between dyslipidemia and cholesterol levels in children. A systematic literature review was performed to identify studies investigating the association between dyslipidemia and asthma in children. The PubMed database was searched for articles published from January 2000-March 2022. Data from a cohort study using electronic health records from 5 hospitals, converted to the Observational Medical Outcomes Partnership Common Data Model (OMOP-CDM), were used to identify the association between total cholesterol (TC) levels and asthma in children. This cohort study used the Cox proportional hazards model to examine hazard ratio (HR) of asthma after propensity score matching, and included an aggregate meta-analysis of HR. We examined 11 studies reporting an association between dyslipidemia and asthma in children. Most were cross-sectional; however, their results were inconsistent. In OMOP-CDM multicenter analysis, the high TC (>170 mg/dL) group included 29,038 children, while the normal TC (≤170 mg/dL) group included 88,823 children including all hospital datasets. In a meta-analysis of this multicenter cohort, a significant association was found between high TC levels and later development of asthma in children <15 years of age (pooled HR, 1.30; 95% confidence interval, 1.12-1.52). Elevated TC levels in children may be associated with asthma.

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

ObjectiveTo 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 methodsTwo 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. ResultsFourteen 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. ConclusionThe 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.