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Epic User Web , Epic ETL documentation/scripts

(Lisa Schilling) #1

Hi all, I know many OHDSI users are creating ETL scripts/documentation from Epic Clarity and Caboodle (formerly Star and Cogito). Although the Epic models are proprietary, I recall being informed that we could post ETL scripts in the Epic UserWeb since this is available only to Epic users. I could have sworn that I once found some of this info on the UserWeb but I checked recently and did not find anything. Regardless, I do think that posting to the EpicUserWeb would be a great idea to help facilitate OMOP/OHDSI use among Epic users. I wanted to get the communities thoughts and knowledge around this. Thanks! Lisa


Hope to know more too.

(Jeselyn Rhodes) #3

Greetings! I am also interested in the availability of OMOP/CDM tools for use with Epic generated data. To-date, I have been unsuccessful in finding documentation or mention of CDM on Epic User Web. Are there any users within the OHDSI community with experience CDM implementation using Epic data?

Kind regards,

(Lisa Schilling) #4

Hi all,
I have asked Epic to set up an area where we can share Epic ETL to OMOP scripts. I had a conversation with them in the spring’17 and followed up recently as there has been no action. They have done this for i2b2- but this may have been done awhile ago. I do wonder if their willingness has changed due to Epic Cosmos, and hence the inertia. @Jes_Rhodes it seems that many of us could share of the work we’ve done as there a lots of folks in the OHDSI community who transform Epic source data to OMOP. @mgkahn, @MPhilofsky - can we share UC/UCHealth work? I’ll check with another project too.

(Don Torok) #5

I would like access to the Epic web site. Is there a way you can sponsor

(Jeselyn Rhodes) #6

Thanks @schillil and all others who may consider sharing their Epic to OMOP experiences! Will the share area be in UserWeb?

(Lisa Schilling) #7

Well @Jes_Rhodes, I don’t have it all sorted out with Epic yet, but yes EpicUserWeb would be the plan–maybe in the data handbook section, but there was some other area the Epic Verona folks had mentioned too. We’d like to be able to see that the non-Epic customers, who consult with Epic customers, such as @DTorok, could have access. Epic has been against this in the past- the EpicUserWEb is only accessible by Epic customers- but there is no incentive for consultants to participate, if they are not able to access and share info. Granted, we have other ways of sharing-email, etc, but it would be a benefit if an Epic user searched OHDSI or OMOP and found information about data transformation/ETL.

(YGW) #8

We are starting a project to map EPIC/Clarity to OMOP. I searched EPIC/Web and there is no information. Did you have any updates on this topic?

(Gregory Klebanov) #9

@yguilarte - we do have experience in this space and do EPIC conversions for our customers. While there are certainly commonalities, every EPIC implementation is somewhat unique and requires dedicated analysis and mapping. Happy to help - feel free to ping me at gregory.klebanov@odysseusinc.com

(David Dorr) #10

Epic expressly forbids this. You need to be a contractor or an employee. Sorry about that.

(Lisa Schilling) #11

Hi all (@dorrd, @yguilarte, @Jes_Rhodes, @jon_duke, @DTorok )
I investigated with Epic about how we could share ETL scripts among Epic users last year. Because the Epic db are proprietary, we cannot post ETL scripts in a public open repository, but we can post them in Epic’s repository on the UserWeb. As @DTorok stated, this is only available to Epic Users with an account, and not consultants, and consultants may not want their work posted. If Epic users do start to post their ETL scripts, it would be nice to have a convention for naming the files it should include OMOP (so users can find it with the search), the extraction db and version and the OMOP db version. It would also be helpful to include a README to provide any details about the progress of the work, considerations, etc- if that is possible. i2b2 users post information in this same place.

Here is the recommendation from Steven Van Manen at Epic late last year (which I thought I had posted already, but I did not)
The best place to start would be to upload the ETL Scripts to the Report Repository in the Data Handbook, look for the upload report button. This will allow you to have the most control over what is getting uploaded, and allows
other Epic organizations to search for and use the scripts as well. Like you
mentioned this is where a few customers have also uploaded there i2b2
scripts as well.

Steven Van Manen
| Software Developer | Research


(Jeselyn Rhodes) #12

Thank you, Lisa!

(Sam Martin) #13

Hello All - (@schillil, @dorrd, @yguilarte, @Jes_Rhodes, @jon_duke, @DTorok, @roger.carlson)

We have joined the OHDSI community as a function of our involvement in the All of Us Research Program, but we also hope to use OMOP for additional Research efforts.

Spectrum Health is a health system in West Michigan and we are currently all Epic (since Nov 2017), but have a mix of Epic and Cerner in our legacy data.

  • Cerner: Inpatient: 2001-2017
  • Epic:
    – Ambulatory: ~2007-Present
    – Inpatient: 2017-Present (Much of the Inpt Cerner data is in Epic Clarity for Epic Ambulatory pts.)

As part of our OMOP mapping fo the Epic data, we have been using Epic UserWeb forums to document, update and share our extract ETL and assumptions (also told we couldn’t post Epic details on public forums…). The posts we (@roger.carlson and I) have published are designed to present what we’ve done and gather additional feedback from the community. The central post within the Research Forum serves as an aggregator for table-specific additional threads it is at:


Please review and contribute to those posts. You will need access to Epic UseWeb, but that offered to all Epic customers (go to https://userweb.epic.com/ )

As to the suggestion to use the Report Repository, we considered it but were concerned our ETL code was still under development and had the impression the Report Repository was for more finalized output. We have asked Epic for best approach and will advise if anything changes.

Also as an FYI, below is the general overview I’ve designed for obtaining the full EHR record (legacy and current Epic) for our participants. There are a few items specific to All of Us or internal work, but most is OHDSI/OMOP focused. I welcome additional feedback on this - will be at the 2018 OHDSI Symposium (Bethesda)

Merged OMOP ETL Workflow

Early 2018 Summary Stats

(Sandeep Kataria) #14

Did this effort gather any momentum? I will like to be part of this effort and hopefully move it along. Thanks.

(Melanie Philofsky) #15

I have started an EHR to OMOP workgroup located here. Mapping EHR data to OMOP is very complex. We need to find common solutions together. Join our meetings!