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EHR data to OMOP CDM Work Group


(Melanie Philofsky) #122

Thanks for the catch, @DTorok!

(Melanie Philofsky) #123

Hello EHR WG friends!

Thank you to everyone who participated in the WG presentation topics for 2020 poll.

The topic for this Friday’s EHR WG call is "Discussion: How Visit Occurrence and Visit Detail are implemented, decision on what is the ‘parent’ Visit”.

The CDM WG is reviewing the conventions for every table in OMOP. They discussed Visit Occurrence yesterday. I think this a very timely EHR WG topic.

Please be prepared to discuss your use cases and implementation of the table at your organization. We will use the same Zoom information as posted above.

*EDIT: As always, this discussion is NOT limited to OMOPers with EHR data. I’m curious to see if the Visit Detail table is useful for those with other types of data :slight_smile:


(Melanie Philofsky) #124

Hello EHR WG friends!

I am canceling our meeting Friday, March 20th.

Please ignore the email cancelation. It states our next WG meeting is in May. That is incorrect. The next meeting is Friday, April 3rd. I currently don’t have access to the computer with the original invite

(Melanie Philofsky) #125

Tomorrow’s meeting is still on. I would like to discuss covid-19 coding in the EHR. And then open discussion on any topics.

(Kristin Kostka, MPH) #126

@MPhilofsky - can you record this by any chance? I really want to listen in but I am unfortunately able to split multiple ways (still trying to get my twin sister to show up to calls – hasn’t worked yet :laughing: ).

(Hung Do) #127

Hi all,
I am trying to map from EHR to OMOP CDM. Would like to join this meeting. Is it happening on Friday at 10am EST time? (which is 1am Saturday in Sydney). Shall I join using the zoom link above?
Count me in!

(Sebastiaan Van Sandijk) #128

I would also like to join today, have the same question as Hung. thanks, Sebastiaan

(Melanie Philofsky) #129

@hungdo1129 and @Sebastiaan_van_Sandi,

Yes, the meeting is at 10am EST. The Zoom link above is the correct link.


I’ll figure out how to record!

(Melanie Philofsky) #130

Thank you everyone for joining today! Our next meeting will be on Friday, April 17th at 10am EST. Since the guidelines are rapidly evolving for encoding covid-19 Conditions/diagnoses and Measurement/lab tests in the EHR, I would like to continue our discussion at our next meeting. Please review how your EHR data is coded for covid-19 up until March 31, 2020 and then how it is coded on April 1, 2020 and later. The CDC has two separate recommendations for coding depending on the date of diagnosis and we should see a change in the representation of a covid-19 diagnosis in our data. How the data is coded in the EHR will play a significant role on how to possibly change your ETL to account for and capture this new way of coding for ETL to the CDM.

The CDC guidelines valid from February 20, 2020 through March 31, 2020 are found here

The CDC guidelines for coding beginning April 1, 2020 are here

OHDSI guidelines for mapping source concepts to standard concept_ids are here

We should see Athena updated to include the most recent ICD10CM code, U07.1, for covid-19 in the very near future.

*Edited to provide the correct 3rd link

(Andrew S. Kanter, MD MPH FACMI FAMIA) #131

Sorry I missed it. Was the meeting recorded as requested? Is there a link?
One of the challenges will be to keep up with all the changing code requirements. I keep releasing versions of the CIEL dictionary with updated maps as they change.

(Kristin Kostka, MPH) #132

I think you meant to link to: https://github.com/OHDSI/Covid-19/wiki/Release

(Melanie Philofsky) #133

Good catch! Thank you, @krfeeney! I updated the link in my post.

I am creating a WG page on the wiki. Once it has been created, I will upload the recording @Andy_Kanter and post the link on this thread.