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EHR data to OMOP CDM Work Group

Hello EHR WG friends,

Our next meeting will be June 25, 2021 at 10am Eastern Time. We will be discussing drug infusion data, specifically drug infusion where dose per a measure of time is the variable of interest in the study. Typically in OHDSI network studies, the total dose is the variable of interest. How do we represent this data in the CDM?

@Andrew @clairblacketer @Christian_Reich @burrowse

Hello. I want to see if I am in the right place here. I work for UTHealth School of Biomedical Informatics as a Programmer and I have been tasked with submitting our data to join the All of Us program. We get our data from Epic EHR. And I see that All of Us is using OMOP CDM. This is the first time anyone on our team is doing this, so the process has not been done before. I was “Googling” to see if EHR to OMOP CDM had been done before to see what the process is or if there are scripts to help this.
I found a github with the sql table creations but nothing with the ETL process. Would this group be somewhere that I could get help with the ETL process? I am not really sure where to begin… I learn well by example so I probably just need to know the process of how to go about this and I might be okay to at least get started and get an understand of what is going on. Anyway, thanks in advance.

My email is Brian.Shukwit@uth.tmc.edu

Thank you.

You are in one of the possible ‘right’ places. Others will be Chapter 6 Extract Transform Load, in the Book of OHDSI,Chapter 6 Extract Transform Load | The Book of OHDSI and the Epic internal forum site. The OHDSI CDM tries to capture, from the patients point of view, their interaction with the medical system, e.g their diagnoses, procedures performed, hospital visits … So before thinking about OHDSI, you need to understand the EPIC data. Can you follow a patient’s story in EPIC, determine when they visited a doctor, what were their diagnoses, any procedures, lab tests (and results) , medications. Once you know how to get a patient’s information from EPIC, getting it into OHDSI will be somewhat formulaic.


We at Spectrum Health are also putting Epic data into OMOP for All of Us. We have been documenting our code on Epic’s UserWeb, since Epic frowns on posting Epic specific code anywhere else. You can find ER Diagrams, SQL Code (SQL Server), and mappings here:

OMOP: TNG (The Next Generation)

Also, All of Us has a new Resource page:

Of course, none of it is guaranteed correct or complete, but it’s a place to start.


You could also look at the course on the EHDEN Academy - the ETL learning pathway we use to train small-to-medium-sized enterprises in the project, and it’s free for anyone to enrol.


Thanks! I’ve emailed them twice to try and get access to Epic’s UserWeb so, still waiting on that. I think this is exactly what I need. I appreciate the help.

Thank you. I’m reading it right now. I appreciate the help.

Thank you Roger for sharing the codes! I am with Sanford Health and we are using EPIC. Your program codes are valuable. One question: do you de-identify your data when etl’ing?

We do not de-identify data beyond what is built into OMOP.

I am cancelling the July 23rd EHR WG meeting. We will meet again on August 6th.


I’m researching accelerators to map Epic EHR data into OMOP. My team is researching User Web for options but is not able to find much material. I came across this forum and see lots of valuable info from the past 2 years. I would like to join the EHR WG meetings. Is there a latest link I can subscribe to and get on these calls?


You can find references to Work Group meetings at Upcoming Working Group Calls – OHDSI

You can sign up to join a Work Group from the OHDSI home page Working Groups – OHDSI under Join OHDSI in MSTeams/Pick a Workgroup.

Regarding next EHR data to OMOP meeting:
Electronic Health Record WG: Friday, Sept. 17 at 10 am ET (Meeting Link)
Meetings are traditionally scheduled for every other Friday at 10 am ET.

Hello all,

Our next Work Group meeting is tomorrow, Friday, October 1st at 10am ET. Please use this link to join our call. We will discuss the following:

  • an expansion or redefinition of the EHR WG scope
  • change the call to another day of the week to accommodate more collaborators

Tomorrow on the EHR Working Group call, Lee Evans will discuss Docker.

Please join us in MSTeams!

The Electronic Health Record working group will be meeting tomorrow to discuss

  1. OKR’s where are we?
  2. Expansion of our OKR’s

Please join un in MSTeams

Hello EHR WG friends,

We are taking a poll to see if another day of the week will work for our meeting. Please vote here.

Jonathan Scheer
Eastern Time

Welcome to OHDSI @jonatron!

You can sign up for the EHR group and all other groups here. You don’t have to sign up and can always join calls without signing up, but by joining a working group, you’ll be added to the space in MS Teams.

Hello all,
Tomorrow morning we will meet at 10am Eastern Time here in MS Teams. Alex Efimov will give a demo of Perseus. Here’s his poster on Perseus: “Perseus”: Design and run your own ETL to CDM – OHDSI

Please complete the poll above for our WG meeting day. Thanks!