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EHR data to OMOP CDM Work Group

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(Manlik Kwong) #142

Hi - Here is an example. I would create a new vocabulary where vocabulary.vocabulary_id = “PH100C” to represent the Philips ECG program version C. One of the concept defined would be for “Electrical Alternans” so the concept entry would look like:

concept_id = 1234567890
vocabulary_id = “PH100C”
concept_name = “Isoelectric delta in lead V5”
concept_code = “V5 ISO DELTA”

measurement.measurement_concept_id = 1234567890
measurement_source_value = “PageWriter TC70: SN 11223344”

I probably would not enter anything in measurement_source_concept_id as the measurement_source_value would have the information for me to trace back to the electrocardiograph that produced the measurement.

You can use the episodes for hypotension/tachycardia/etc - my first inclination is that mapping such statements to OMOP would end up in the Condition table. Unless I know when the tachycardiac started and ended - I would not have enough information to register an episode. If it is at minimum registered in Condition_Occurrence - you can at least search on it and see within which visits (thus time) it was observed.

All my ECG statements are mapped to the Condition_Occurrence table.


(Antoine Lamer) #143

Thank you for your answer !

Yes, in our case, we also have start and end date, as well as other derieved values : extreme value, mean value etc …


(Melanie Philofsky) #144

Hi @AntoineLamer and @MathildeFruchart,

Welcome to the EHR WG!

Yes, today is an open discussion, so we can definitely discuss your questions. The details to join the meeting are listed on the WG page and further up in this discussion thread.

Cheers,
Melanie


(Melanie Philofsky) #145

Hi @mkwong,

Would you please clarify? You give your source data

But then you map them to the Condition table?

I think I am missing something. Why give them “Measurement” concept_ids and source values and then put them in the Condition table?


(Manlik Kwong) #146

Hi,

Sorry for the confusion in my example.

Electrocardiographic data - those that come from a standard 12-lead ECG contains measurements (ex. V4 R-wave amplitude) and computerized diagnosis statements (ex. Normal sinus rhythm) automatically generated from the electrocardiograph device. All the measurements that are numeric amplitudes, durations (ex QRS Width), and counts (ex 5 PVCs) all go into the measurements table as LOINC concepts where possible.

All computerized interpretation statements are mapped if possible to the Condition table as SNOMED concepts. For example the computerized interpretation statement from the electrocardiograph “Atrial premature complex, SV complex w/ short R-R interval” from a Philips TC70 would be mapped to the Condition_Occurrence table as:

condition_occurrence.condition_concept_id = 4141030
condition_occurrence.condition_source_value = “PH100C.Atrial premature complex”

Hope that helps.


(Dan O'Leary) #147

My interest is information about the device. You say, for example, “Electrocardiographic data - those that come from a standard 12-lead ECG contains measurements (ex. V4 R-wave amplitude) and computerized diagnosis statements (ex. Normal sinus rhythm) automatically generated from the electrocardiograph device.”

Do you record the device that provides the information? If so, at what level? Is it just make and model (Philips TC70) or other information such as serial number, software version number, etc. Some of this information is encoded in the UDI on the instrument. Do you use the UDI?


(Manlik Kwong) #148

Hi,

Re device - the data that comes over our interface include the device serial number, model, and analysis software version - both measurements and computerized interpretation algorithms. I don’t think the UDI information is included in the patient record. This is the same for defibrillator devices in pre-hospital settings too.


(Melanie Philofsky) #149

Hello EHR WG friends!

Tomorrow, Friday, May 29th, we will discuss @AntoineLamer & @MathildeFruchart use case for mapping peri-operative data into the OMOP CDM.

Please join us at 10am EST. The meeting details are found here.


(Melanie Philofsky) #150

Hello EHR WG friends!

Friday, June 12th we will discuss CDM V5.3 to v6 transformation experiences. I encourage all collaborators to join the call since this topic is not EHR specific. We can all learn from other’s experiences!

Please join us at 10am EST. The meeting details are found here


(Melanie Philofsky) #151

The next EHR WG will be held Friday, July 10th at 10am EST. We will be discussing “How collaborators map custom codes to standard concept_ids. The two main options include: Source to Concept Map table or use of Concept/Concept Relationship tables”.


(Nuno André Da Silva) #152

Hi all,
My name is Nuno and I am very green in OHDSI. In my hospital, in Lisbon, we are currently thinking about implementing the OMOP CDM on top of our EHR for research. Our EHR is based on Cerner (Siemens) Soarian Clinics. When I search for those key words nothing showed up. Is there someone working or that worked with the topic?
Thank your for your time,
Nuno


(Melanie Philofsky) #153

Hello @nuno.andre.da.silva,

Welcome to OHDSI!

There was a Cerner working group a couple of years ago, but it hasn’t been active in a while.


(Melanie Philofsky) #154

Hello EHR WG friends,

Tomorrow, Friday July 10th we will discuss: “How collaborators map custom codes to standard concept_ids. The two main options include: Source to Concept Map table or use of Concept/Concept Relationship tables”.

The Zoom meeting details to join are located on the WG page here.


(Don Torok) #155

Try https://github.com/OHDSI/ETL-CDMBuilder/tree/master/man/CERNER.


(Melanie Philofsky) #156

Hello!

Friday, July 24th at 10am EDT we will discuss “How to define the Observation Period for EHR data”. The current ETL conventions for the Observation Period are found here and the updated conventions discussed by the CDM/Vocabulary WG are found here. We will use both of these as a starting point for our discussion. Since this topic is brought up often from those with EHR data, I think it would be beneficial for us to discuss and possibly add some more guidelines for the CDM/Vocab WG to consider on how to create a more accurate Observation Period from EHR data. Along with our usual EHR collaborators, I would like to invite @krfeeney, @Christian_Reich, @Chris_Knoll, @Vojtech_Huser, @Patrick_Ryan, @cukarthik, @Andrew, and others to the discussion. A comprehensive set of views is needed to fully understand the implications for any decisions made on this logic.

Meeting details are above. The forum won’t let me repost the meeting details here since they are “too similar” to what I’ve already posted.


(Kristin Kostka, MPH) #157

Hi @MPhilofsky!

This is a great topic. We talk about this a lot in the N3C program.

To start, here’s what we put in our FAQ for our OMOP sites:

Sites often ask if the OBSERVATION_PERIOD table is required. The OBSERVATION_PERIOD is a table that is required for downstream analytics. It establishes, as best as we are able, a valid period of time that someone is observed in a database. Since each data asset/data partner usually has different understandings of how their patients move in and out of their system we don’t have a good “rule of thumb” for how to define an observation period in mass. Essentially, it should be the time period where you are reasonably confident that any interaction with the health care system would be captured in the data. Therefore, we really want sites to do this themselves because they know their data best.

Maybe @ericaVoss or @clairblacketer can hop in tomorrow’s discussion too. They’re both people I regularly consult with as we talk about the best practices for constructing this logic. (Spoiler: we don’t have a silver bullet here.)

P.S. The forum says I’ve replied to you a lot in this chain, maybe I should reply to someone else :wink:


(Andrew Williams) #158

I regret that I won’t be able to join due to a conflict but thanks so much for your leadership in this important area Melanie! I look forward to finding out about the progress this group will make.


(Tim Quinn) #159

Hello @MPhilofsky – We at the Icahn School of Medicine at Mount Sinai (ISMMS) are preparing to embark on the journey to load OMOP from Epic Caboodle. We’ve had a few knowledge-sharing calls already with several members of the incredibly helpful and generous OHDSI community: Roger & Sam at Spectrum Health; Michael, Ufi, and Anoop at HDC; and Brian, Steve, and Kent at UC Davis. (As a newbie, your forum prevents me from @-tagging them.) Are there any enrollment steps for joining the EHR WG, or do we simply join the bi-weekly Zoom? Looking forward to engaging with everyone!


(Don Torok) #160

Just come to the zoom meetings. If @MPhilofsky is maintaining a members list, you can ask her to add you during the meeting. Welcome aboard.


(Melanie Philofsky) #161

Welcome, @quinnt!

Yes, as @DTorok said, please join us via the Zoom link above. There isn’t a formal list or “membership”, the calls are open to all. I try to post the call topic before our meetings. The next meeting will be Friday, August 21st 10am ET


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