Myself and my colleagues @pbiondich and @Nethmi_Rodrigo (who posted some questions here) are from the OpenMRS (Medical Record System) community.
About OpenMRS: OpenMRS is an open-source, community-driven electronic health record (EHR/EMR) system. It’s designed particularly for resource-constrained environments like Low- and Middle-Income countries. OpenMRS is used in over 80 countries and has been used in the care of >22 million patients. Over 4,000 articles have been published that used OpenMRS for various forms of research.
Why We’re Excited about OHDSI and the OMOP CDM: We want to make our EMR’s data easier for researchers to use. But Researchers around the world face many obstacles, but this is especially true for Researchers in resource-constrained settings.
Specifically, we plan to:
use/map OpenMRS’ custom data model to the OMOP CDM, and then;
set up a re-useable open-source tooling pipeline for data to be extracted for research question use (i.e. configurable OpenMRS ETLs).
Looking for Help Here
There are two main ways we are seeking OHDSI community interest in this project:
Seeking Help on The Technical Side: We’re running into some challenges visualizing data with Atlas, and we’d love input here: Help with visualizing data in Atlas
We want to talk to Researchers! We are looking to interview: Researchers and Program Decision Makers; e.g. Researchers like Epidemiologists, Health System Strengthening, Public Health, Whole-Health/OneHealth, etc; and Program Decision Makers like Population/Public Health leads. If you or anyone you know fits that role, please let me know! We will ask about their experience as a Researcher in general. (OpenMRS-data-experience is nice to have but not required.)
We would love to hear from you and learn from you. Or, if there are any other researchers or people you think we should speak with, please let us know!
Thanks specially to Book of OHDSI co-author Kristin Kostka for the insights she’s already been sharing
Our Progress so Far
So far we’ve made some great progress building this pipeline:
We’re using a tool called SQLmesh to handle the transformation from our usual supported databases (more on that in the Engineering notes linked above)
We’ve already built components that can convert OpenMRS data to major OMOP entitites.
Next Up:
We are excited to use OMOP supported tools like Atlas to visualize the extracted data.
Our next big goal is to complete the conversion for all the other entities and build an out-of-the-box pipeline that can transform OpenMRS data to the OMOP format to be used anywhere it’s needed.
@grace_potma Thanks for sharing your work! I just started in a new role earlier this month and will be transforming my institution’s data into the OMOP CDM. We’re still considering our tooling and I noticed you’re using SQLMesh so was curious to learn if you also considered other related tools (like dbt), the deciding factors in using SQLMesh, and how using it has been going? Thanks for sharing from your experience!
@grace_potma@pbiondich Alexander Davydov recently shared your post with me.The OHDSI Africa Chapter would be very interested in what you are doing in the space of OpenMRS ETLs to the OMOP CDM. Please come to the next OHDSI Africa Chapter meeting on Jun 23 at 10 am EDT. W have allocated some time on the Agenda to discuss what you are doing. The Chapter has members from many different sectors who would be able to help with #2. As for #1, the OHDSI Community meetings this month have been devoted to different functionality of ATLAS. Perhaps answers to your questions can be found in the recordings. Otherwise, contact Chris Knoll.
@Nethmi_Rodrigo pls see msg above. Forum posts only allow tagging 2 people per message! @Alexdavv See above, invitations to Grace, Paul and Nethmi to join the next OHDSI Africa Chapter meeting
At the meeting, we would also like to discuss whether you have encountered vocabulary in OpenMRS databases that did not have standard OHDSI concepts. Have you compiled a list of those concepts?
