ArticleJournal of biomedical informatics2022
Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration.
Article in Journal of biomedical informatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it, 27 citations in OpenAlex.
- Common data models and data standards for tabular health data: a systematic review.BMC medical informatics and decision making · 2025Pooled it
- Article
- Expanding the OMOP common data model to support extracorporeal life support research.JAMIA open · 2026Article
- A Practical Approach to Assessing the Completeness of Electronic Health Records for Medical Research: Data Quality Study.JMIR medical informatics · 2026Article
- Article
- Mapping Emergency Medicine Data to the Observational Medical Outcomes Partnership Common Data Model: A Gap Analysis of the American College of Emergency Physicians Clinical Emergency Data Registry.Journal of the American College of Emergency Physicians open · 2025Article
- Exploring the integration of medical and preventive chronic disease health management in the context of big data.Frontiers in public health · 2025Review
- 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.Frontiers in digital health · 2025Article
- Decades in the Making: The Evolution of Digital Health Research Infrastructure Through Synthetic Data, Common Data Models, and Federated Learning.Journal of medical Internet research · 2024Article
- Knowledge abstraction and filtering based federated learning over heterogeneous data views in healthcare.NPJ digital medicine · 2024Article
- FOUNTAIN: a modular research platform for integrated real-world evidence generation.BMC medical research methodology · 2024Article
- Converting OMOP CDM to phenopackets: A model alignment and patient data representation evaluation.Journal of biomedical informatics · 2024Article
- European Health Data & Evidence Network-learnings from building out a standardized international health data network.Journal of the American Medical Informatics Association : JAMIA · 2023Observational
- The Journey of Data Within a Global Data Sharing Initiative: A Federated 3-Layer Data Analysis Pipeline to Scale Up Multiple Sclerosis Research.JMIR medical informatics · 2023Article
- Cardiovascular Care Innovation through Data-Driven Discoveries in the Electronic Health Record.The American journal of cardiology · 2023Review
- Using A Standardized Nomenclature to Semantically Map Oncology-Related Concepts from Common Data Models to a Pediatric Cancer Data Model.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2023Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 1 country.
Funding
Abstract
objectiveThe large-scale collection of observational data and digital technologies could help curb the COVID-19 pandemic. However, the coexistence of multiple Common Data Models (CDMs) and the lack of data extract, transform, and load (ETL) tool between different CDMs causes potential interoperability issue between different data systems. The objective of this study is to design, develop, and evaluate an ETL tool that transforms the PCORnet CDM format data into the OMOP CDM.
methodsWe developed an open-source ETL tool to facilitate the data conversion from the PCORnet CDM and the OMOP CDM. The ETL tool was evaluated using a dataset with 1000 patients randomly selected from the PCORnet CDM at Mayo Clinic. Information loss, data mapping accuracy, and gap analysis approaches were conducted to assess the performance of the ETL tool. We designed an experiment to conduct a real-world COVID-19 surveillance task to assess the feasibility of the ETL tool. We also assessed the capacity of the ETL tool for the COVID-19 data surveillance using data collection criteria of the MN EHR Consortium COVID-19 project.
resultsAfter the ETL process, all the records of 1000 patients from 18 PCORnet CDM tables were successfully transformed into 12 OMOP CDM tables. The information loss for all the concept mapping was less than 0.61%. The string mapping process for the unit concepts lost 2.84% records. Almost all the fields in the manual mapping process achieved 0% information loss, except the specialty concept mapping. Moreover, the mapping accuracy for all the fields were 100%. The COVID-19 surveillance task collected almost the same set of cases (99.3% overlaps) from the original PCORnet CDM and target OMOP CDM separately. Finally, all the data elements for MN EHR Consortium COVID-19 project could be captured from both the PCORnet CDM and the OMOP CDM.
conclusionWe demonstrated that our ETL tool could satisfy the data conversion requirements between the PCORnet CDM and the OMOP CDM. The outcome of the work would facilitate the data retrieval, communication, sharing, and analysis between different institutions for not only COVID-19 related project, but also other real-world evidence-based observational studies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.