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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


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