Development of an OpenMRS-OMOP ETL tool to support informatics research and collaboration in LMICs

Juan Espinoza*, Sab Sikder, Armine Lulejian, Barry Levine

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Background: As more low and middle-income countries (LMICs) implement electronic health record systems (EHRs), informatics has become an important component of global health. OpenMRS is a popular open-source EHR that has been implemented in over 60 countries. As in high income countries, interoperability and research capabilities remain a challenge. The Observational Medical Outcomes Partnership (OMOP) is one of the most relevant common data models (CDM) to support EHR-based research and data sharing, but its adoption has been limited in LMICs. To address this gap, we developed an OpenMRS to OMOP extract, transform, and load (ETL) tool using Talend. Methods: We built on existing documentation to develop a comprehensive concept map from OpenMRS to OMOP. The OMOP domains were reviewed for overlapping concepts in OpenMRS, and a core set of tables were selected for ETL development. Specific variables were then identified from OpenMRS tables which mapped to OMOP domain fields. Afterwards, the ETL tool was developed using MySQL Workbench, PostgreSQL, and Talend. Results: Seven of 14 OMOP domains were selected for ETL pipeline development. The location, person, and provider domains required the least amount of Talend job components, which involved ≤2 tDBInputs, 1 tMap, and 1 tDBOutput. Care_site, observation_period, observation, and person_death all required additional Talend components to properly transform the respective data fields. It took 15 min to transform 9,932 OpenMRS observation records to OMOP. Conclusions: It is feasible to develop a free, open-source ETL pipeline to transform clinical data in OpenMRS instances into OMOP. Processing large datasets is swift and scalable with potential for more improvement. Using this tool alongside OpenMRS can dramatically increase the potential for global health informatics collaborations and building local infrastructure and research capacity. Further testing and development will be required prior to widespread dissemination, along with appropriate documentation and training resources.

Original languageEnglish (US)
Article number100119
JournalComputer Methods and Programs in Biomedicine Update
Volume4
DOIs
StatePublished - Jan 2023

Funding

This project was supported by an anonymous gift. JE's time is supported in part by grants UL1TR001855 and UL1TR000130 from the National Center for Advancing Translational Science (NCATS) of the U.S. National Institutes of Health. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Keywords

  • ETL pipeline
  • Global health
  • OMOP
  • OpenMRS
  • Research informatics

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • Biomedical Engineering
  • Computer Science (miscellaneous)
  • Computer Science Applications

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