OHDSI Home | Forums | Wiki | Github

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.

(Melanie Philofsky) #134

Hello EHR friends!

Tomorrow at 10am EDT will be our follow up call on covid-19 coding in the EHR. The new CDC covid-19 recommendations for coding the Condition with ICD10CM codes was updated on April 1st. If you have run an ETL since then, you should have the new U07.1 code in your data. Covid study questions are evolving quickly. Researchers are/will be seeking data on intubation, ventilation, dialysis and ECMO. These data live in many different places of varying granularity in the EHR. And map to multiple CDM tables depending on the “meaning” of the data. If you have these data in OMOP, I would like you to share with the group. A few questions to answer: Are the data structured or unstructured, the source domains, the target domains, the research questions you think these data can answer, and any knowledge on data gaps whether there is a gap in standard concept_id representation or gap in what happens at the bedside versus what is being ETL’d to the CDM. All experiences are welcome! This will be a good learning opportunity for us all.

The link to the meeting is further up in this forum chat. I look forward to a good discussion tomorrow. And I will record the meeting for those not able to join.

(Melanie Philofsky) #135

Hello EHR WG!

This Friday the topic of discussion will be

“Discussion: Drugs order/administered/dispensed/med rec how this is recorded, how well it is captured, what insights are gleaned”

The Drug Exposure domain is one of the most frequently used tables for research. If you have ETL’d Drug data into the CDM, please attend to discuss and inform our colleagues.

Meeting details can be found on our Wiki page located [here]. I look forward to talking with you on Friday @ 10am EDT!


(Robert Schuff) #136


Could I get added to this workgroup? We are implementing an OMOP 5.3 - based COVID data mart from our Epic data and wopuld love to join/contribute where I can.



(Antoine Lamer) #137

Hi !

@MathildeFruchart and I are working on the implementation of peroperative data into OMOP CDM. We are developping an algorithm to detect hypotension, tachycardia, etc …
We’re wondering where to store the outputs of our algorithm (Some questions here).

Would it be possible to add this point to the agenda of tomorrow meeting ?

(Manlik Kwong) #138

Hi - I have both derived and non-standardized data (ex electrocardiograph measurements and statements) that do not map well to LOINC or SNOMED. These go in the same places as all other measurements and observations - just using a custom vocabulary and concepts.

(Anna Ostropolets) #139

@mkwong this is very interesting! Could you please share some of the ecg concepts that won’t map to loinc? We we’re able to map ours and ecgs are pretty standard, so I’m wondering what those look like

(Manlik Kwong) #140

Hi - I have a daily feed of all 12-lead ECGs taken throughout Tufts Medical Center in which all the measurements and computerized interpretation statements are mapped to our OMOP_ECG warehouse. Each manufacturer - Philips, GE, GLASGOW, etc have different variations in their ECG measurements and interpretation statements they generate. They all share the usual LOINC concepts - QT/QTc, R-wave amplitude, etc. However, some manufacturers programs produce measurements that others do not. For example Philips PH100/C include Initial and Terminal wave measurements across all 12-leads, QRS Peak-to-Peak or Swing, etc. I have OMOP maps for Philips, GE, and GLASGOW programs.

When I receive the standard 12-lead data - I also derive the X-Y-Z leads and these are all non-LOINC measurements.

Same for the different interpretation statements. All these are captured for doing machine learning types of projects where all measurements and statements are possible features, not just those that were mapped to LOINC or SNOMED.

  • MK

(Antoine Lamer) #141

Do you mean in using only the measurement_source_concept_id, and leaving the measurement_concept_id ?
Would you have some examples of statements ?

In our case, episodes of hypotension/tachycardia/etc look like period/era more than measurement (as for condition era / drug era). That’s why we were thinking about storing them into episode (in OMOP oncology extension)