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Anyone completed a move to CDM v5.4 using EHR as the source data?

Many folks with EHR data are contemplating or in the process of moving to CDM version 5.4. If you have completed the move, the Healthcare Systems interest group would like to hear about your conversion. Effort involved, tools or scripts used, unforeseen delays, etc.

Would anyone like to talk with the group and share your experience? We are a friendly group learning from other’s experience through discussion and collaboration to make the journey a little easier for others :slight_smile:

At the University of Michigan, we are in the process of quantifying the effort to do this work from Epic. I too am interested in hearing from others who are anywhere along the continuum to help inform our project planning process.

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Hi John,

It seems a bit difficult to find and follow workers such as yourself that are at the same stage as others like me to collaborate and share experiences with. Have you found or do you utilize any other resource than this forum?

-Sanjay M. Udoshi MD

Thanks for reaching out on this, Sanjay. I haven’t found any other resources as yet. I do participate in the weekly community calls and the twice a month CDM calls. While interesting, those haven’t provided me much help on the planning journey. We are also reaching out to peer organizations in our PCORI network to see who has been down the OMOP road and can give us some guidance. I’d like to participate in a Starting your OMOP Journey group, yet I don’t have the bandwidth to lead it atm. The catch-22 for me is that I cannot officially start the work until I get approval, which requires an estimate of the effort. I feel that the only way I can get that estimate is to start the work.


As @MPhilofsky stated, please attend our Health Systems Work group meetings. You can get times here Weekly work group calls. The work group has a number of members that have done ETL’s from Epic Clarity and Caboodle.

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Very understandable. It is a bit of a slog, but over the last month I have made significant progress on standing up a development environment. I feel that OHDSI must concentrate future efforts on more turn-key solutions in order to help on-board as many workers interested in OMOP as possible. Right now, it is like being handed a Lego Technic set. Though the instructions are useful, it doesn’t obviate the amount of time and effort required to put all the pieces together.

I have searched for EPIC Clarity and Cerner Millenium example ETLs and I have found none. Where are these shared or are they precluded from sharing from the vendors?

@Sanjay_Udoshi: Totally understand the desire. But the multitude of different technology solutions people use and the variability of technical expertise and ability to debug problems makes this next to impossible for a Open Source community that works on the basis of volunteer work. However, there are turn-key solutions from small consulting shops. You get what pay for! :slight_smile:

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Clarity code is considered Epic IP. As such, it can only be shared amongst Epic customers on the Epic User Web.

For EHR data:

6 months if you’ve done an OMOP ETL before and are fully staffed
9 months if you’re new and fully staffed
Minimum 12 months if only one person is assigned the job

Fully staffed = Full time dev, full time analyst, full time QA/UAT tester starting about 1/4 through the project, a technical architect to set up infrastructure and jobs (time commitment depends on organizational structure) and a PM. Quality will go down significantly if you skimp on any of the resources. Especially the analyst. You need someone who knows the source data and the OMOP CDM.


I can S-T-R-O-N-G-L-Y vouch for @MPhilofsky staffing/commitment recommendation. It took us THREE attempts to get our OMOP ETL right (and it is still evolving). The first time, we tried to totally outsource it to folks who didn’t understand our source data. The second time, we grossly understaffed the effort. The third time, we dedicated resources – technical, infrastructure, domain expertise, and project management. It still took us 6 months, even on our third time around.

If you’re already an Epic customer, we at Spectrum Health posted our ETL code on the User Web here: OMOP: TNG (The Next Generation) (epic.com) Note:This is for v5.3.1, not 5.4.

Melanie’s numbers are good. Working 100% on this project, I was able to get fairly well started in a year. But I’ve spent the last 3 years improving and expanding it.

I would discourage you from thinking of this as a project to complete. It’s an on-going process, more like a data warehouse than an extract. This is just getting the data into OMOP. There’s a whole larger world of processes for getting the data out and using it in research.


I thank everyone for this valuable feedback!

@Sanjay_Udoshi @MPhilofsky @mgkahn @roger.carlson Thanks so much everyone for the great detail on this thread. I apologize for the delay in getting back on this - other priorities. I now have a good estimate of the effort and will advance the proposal. And @roger.carlson I saw your content on the UserWeb. Ty so much for posting that. JB