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EHR data to OMOP CDM Work Group

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#182

@MPhilofsky included my scoring and resisted the urge to add new topics… That said, there is a growing question (tension) that I’m trying to address and I cannot help but believe it has been encountered, and hopefully addressed, elsewhere.

Topic:
How do you effectively offer OMOP to users who’s perspective or analysis is represented by a world bound by a terminology such as ICD-10.
Example: Their population definitions, metrics, quality checks… are all rooted in a single terminology; so when presented with OMOP data, they say “can you show this as ICD-10?” Yet, they want to use OMOP because of its ability to deliver more expansive datasets.

I can understand how they would ask that, but it seems to bypass (or miss) the value inherent to a well established CDM like OMOP.

  • Who else has encountered this?
  • How have others addressed it?
  • Is there another thread/group I should be asking this?

Thanks!

#183

Answer No 1: There is no such a thing as ICD-10. Well, there is, except there are many. Every country has their own. The American version, ICD-10-CM, is the largest with over 100k codes. The original WHO ICD-10 has less than 20k. So, obviously it’s not the same. But even the codes that overlap are not always the same between the versions.

Answer No 2: ICD-10 is suboptimal for research, because it has a lousy one-parent only hierarchy. SNOMED has a way stronger hierarchical organizations, plus other links connecting the concepts.

Answer No 3: There are conditions in other terminologies. For example, HCPCS M1062 “Patient immunocompromised” is a Condition not stored in ICD-10. Internationally you have plenty of those.

Happens often with people who have used their definitions for a long time and don’t want to change their ways. I have empathy.

Just map them using the mapping tables provided by OHDSI. We have all ICD-10s from most versions mapped over.

1 Like
#184

If I had to guess, I’m sure all US EHR data holders have encountered this resistance from within their organization at some point in time. @cukarthik and friends at Columbia have been using OMOP for a long time. He might be able to provide more insight.

Education, education and then more education :slight_smile: The power and beauty of OMOP is in the standardized data model and the terminology harmonization. The one and only one standard concept_id to represent an idea, the hierarchies, the classification concepts, domains to identify the table where the data lives, and the ability to represent your source data ‘as is’ with a 2 billionaire source concept_id make the OMOP CDM amazing!
*The ability to collaborate with like minded people all over the world is implied :slight_smile:

I haven’t delved into Conditions, but I have started an educational series for Drugs. Similar to ICD10CM codes, folks love the NDC codes, but they aren’t standard! The series includes the OMOP basics of mapping source codes to concept_ids, CDM layout, OMOP Vocabulary tables, etc.; a library of SQL queries including how to obtain all drugs with a specified ingredient or all drugs under an ATC classification concept; a video on how to use Athena to identify drugs, ingredients or classifications of interest; a deep dive on our source data and how it fits into the CDM; future plans include Atlas, DQD, and other OHDSI tools. And it is all catered to our local users. Colorado is still in the implementation phase of this learning initiative, so the results aren’t final. RxNorm and Drugs have been well received. Say goodby to the huge time waste of string text searches on multiple source data tables!

Thank you for not adding more topics, @samart3! The EHR WG does have meetings without an agenda, so folks can bring any idea/concerns/questions to the WG for discussion. And the forums are the best place to discuss topics that involve more than EHR specific data.

2 Likes
#185

FYI to @MPhilofsky reference of a library of SQL queries. The link to an online version is https://github.com/OHDSI/QueryLibrary. Or you can install R package locally from https://github.com/OHDSI/QueryLibrary.

1 Like
#186

In our experience getting folks to change things regarding their EHR reminds me of the Charleston Heston “my cold dead hands”. Even the place we are partially owned by has told us to take a walk.

#187

@Christian_Reich thank you for the answer and also thank you for calling me out on my use of “ICD-10.” I was attempting to be generic, but should have been more specific (ICD10CM).

I think much of it is exactly as you said, they are using familiar population definitions (by habit or mandate) and it has limits their perspective.

@MPhilofsky your perspective was also very helpful.

This just increases the importance for us to implement the OHDSI tools for consuming OMOP and building cohorts. Given that our All of US is the primary consumer of our OMOP data, I’ve not needed to focus on socializing/training on end user access to Atlas, Athena and other tools. Without those it will be difficult for our teams to make the leap to OMOP as their native frame for defining populations.

#188

Hello EHR WG Friends! Tomorrow, March 18th at 10am Eastern Time, Christian Reich will present the new, Wide Mapping Table during our call. Check out this forum post or this one or this one for some more information on this future feature.

Wide MAPPING table (in vocabulary) (problems with relationship)
#189

It must be today or 19th :wink:

#190

Yes, Friday, March 19th! I just can’t wait!!!

#191

Hello all! Our next meeting was scheduled for April 2nd, Good Friday. I have cancelled this meeting since this is a holiday for some. Our next meeting will be held Friday, April 16th.

#192

Hello everyone,

Our next meeting is this Friday from 10am - 11am Eastern time. We do not have an agenda or presentation, so it will be an open discussion. All ideas/concerns/questions on EHR data, ETL, the CDM, OHDSI tools, or anything of any relation to observational research is welcome!

1 Like
#193

Our next meeting is this Friday, April 30th at 10am EST on MSTeams. We will discuss the proposed changes from CDM v5.3 to v5.4 in order to provide feedback to the CDM WG.

#194

@faramarz
Faramarz Amirshahi
faramarz@vectorinstitute.ai
EST

#195

Welcome @faramarz to the EHR working group!

You can sign up for the EHR WG and an OHDSI MSTeams account here.

And here’s the link to the EHR WG space on MSTeams.

#196

Reminder: Tomorrow May 14th at 10am Eastern Time, we will NOT meet in the EHR WG space. We be joining the Clinical Trials working group call on MS Teams.

#197

Our next meeting is this Friday, May 28th at 10am ET on MSTeams. We will discuss how to implement our OKR Key result #1, Maintain an up-to-date list of educational and collaborative resources on MSTeams site for those OMOPing data to the CDM, and have an open discussion period

#198

Our next meeting is this Friday, June 11th at 10am ET on MSTeams.

Presentation by Paul Nagy - FHIR to OMOP: What is FHIR, how does FHIR relate to OMOP, what are OHDSI and FHIR doing together?

1 Like
#199

Hi @MPhilofsky - can anyone join the presentation tomorrow, or only the WG participants? If yes, do have a link?

Many thanks.

Nige.

#200

Yes, our meetings are open to everyone. Here’s the link :slight_smile:

#201

Thanks!

t