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EHR data to OMOP CDM Work Group


(Melanie Philofsky) #1

I had the pleasure of meeting many new OHDSI friends at the Symposium that are also struggling to accurately map their EHR data to the OMOP CDM. I would like to form a working group that would meet to discuss these issues and then come up with conventions. Here’s a couple problems that come to mind:

  1. The medication administration record (MAR) contains data for continuous infusions with varying amounts of drug given per minute or hour. Inotropes, sedatives, anesthesia, insulin, etc. are titrated to effect. Do we roll up a single medication into one Drug Exposure record? i.e. the patient received X amount of drug from the start to end date. Do we take each individual source record and create one record in the CDM? i.e. the patient received X amount of drug from 8am to 10am, then X amount of drug from 10am to 11:12am, the Drug X was held for 46 minutes, and restarted at 11:58 to 2pm and X amount was given. Do researchers need to know the varying dosages 5 mcg/kg/min or 10 mcg/kg/hr?

  2. Another discussion that came up is how to correctly map visits to one of the visit_concept_ids and map face to face Visits to the CDM? EHR source data may describe a visit as a “surgery” and surgery may happen during inpatient or an outpatient visit.

  3. I’ve noticed that in 4 separate EHR datasets I have worked with, ~15% of drug records only contain an internal identifier. These internal identifiers do have a text string, but mapping thousands of text strings using Usagi is a very time consuming process. Do others have this issue? Have others found a solution? Should we work together to identify a solution? And why the heck is this happening? These are all different types and classes of medications. Sometimes these aren’t true drugs, but are ordered like drugs (breast milk, needles, oxygen). But many times these are drugs that map to standard drug concepts.

If you are interested in joining, reply to this thread with your name, email and time zone. Once I get a list of emails and time zones, I will send out a poll to get these meetings started!

Tagging a few people I know are interested: @roger.carlson @Sgp6a @cukarthik @DTorok @Daniella_Meeker @Adam_Black @burrowse @samart3 @mgkahn @Andrew I am limited to tagging 10 persons per post. Please forward to others that are interested!

Conventions on visit and observation _end_datetime for death
(Maxim Moinat) #2

Hello Melanie, I would like to contribute to this working group. We have some experience with European EHR data.
One suggestion is to make it a new subgroup of THEMIS, as we should publish the results in the same way. Have you thought about this already?
(maxim@thehyve.nl, CEST)

(Melanie Philofsky) #3

Great! I’ll add your name to the list.

Yes, this is part of Themis and @Frank’s Work Group for working groups. We need to ensure that solutions work for the community!

(Don Torok) #4

Don Torok, dtorok@ephir.com, eastern time.

(Christian Reich) #5

Haven’t we solved and discussed this already?

Will release a new comprehensive Visit hierarchy soon. You should check it out.

One idea that’s floating, but needs somebody to take it on, is the public mapping website, where this can accumulate across many users. We need money or volunteers.

(Melanie Philofsky) #6

Nope, looks like this conversation moved to here and remains unresolved. If it has been ratified, it isn’t here either.

Are you referring to the one @Gowtham_Rao proposed at the beginning of the year? That’s great for data that reliably has a Place of Service code for each Visit. The EHR data I have seen doesn’t always have POS for each visit. :’(


I’ll add your name and email to the WG list. Thanks for volunteering, @Christian_Reich!

(Christian Reich) #7

@MPhilofsky: You got it.

Let’s close it out. Happy for you to push.

Yep. I am working with him on a comprehensive one.

Terrible. We don’t have anybody.

(Steve Patterson ) #8

Happy to be involved. Steve Patterson, sgp6a@hscmail.mcc.virginia.edu, Eastern

(Sam Martin) #9

Yes, I would be interested in joining. At this time @roger.carlson will not join as he is doing all he can to focus on “Epic specific” work like mappings and such. This work will likely inform his extracts, but appears to beginning from more of a general knowledge perspective.

samuel.martin@spectrumhealth.org Eastern time

(Evan Sholle) #10

Please add me, Melanie - evs2008@med.cornell.edu (EST).

(JungHyun Byun) #11

Please add me, Junghyun Byun - lance.byun@gmail.com (GMT).

(Melanie Philofsky) #12

This is a great response! I’ve added @MaximMoinat, @Sgp6a, @LanceByun, @samart3, @esholle, @DTorok, and @Christian_Reich to the list. I’ll give it to the end of the week before I create the meeting time/day poll

(Bell Eapen) #13

Bell Eapen @beapen (Eastern Time)
I am a newbie but would love to join.

Currently working on this (ETL for OS EMRs):

(Steve Lyman) #14

Please add me. Steve stephen.lyman@allscripts.com, eastern

(Melanie Philofsky) #15

Hi all!

I sent out an email with a Doodle poll to those that gave me their email address. And it’s located here for those that would like to join, but haven’t posted to this thread.

(Paolo Eusebi) #16

I just joined ohdsi, hop to be involved. I am involved in seversl projects about italian emr.

(Aelan Park) #17

Please add me.

(Melanie Philofsky) #18

Hi all,

Our first meeting will be on Friday, November 2nd at 8am MT, 10am ET and UTC -07:00. The meeting link is below

The Google Doc with a very short list of issues and goals is here https://docs.google.com/document/d/12ELmThYhw6TJ_FoQpMWVDJ3rMlB5_6BkjPye1W20yUU/edit
Please add to it before our first meeting. And please reach out with any questions, comments, idea, etc

(Melanie Philofsky) #19

We had a good turnout for the first meeting and I know others will be joining at our next meeting on Friday, November 16th at 8am MT, 10am ET and UTC -07:00.

Meeting notes and next week’s agenda are here

Issues, assumptions, and goals document is here

Feel free to reach out about anything above or anything at all

(Sandeep Kataria) #20

I will like to join/contribute as well. Sandeep Kataria email - skataria@uic.edu Time zone - Central Time.
Thank you for starting this.