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Conversion of measurement data beyond laboratory values: conversion of echocardiography into OMOP-CDM


(Seng Chan You) #1

Hi all,

I’ve just converted data of echocardiography into OMOP-CDM.
The mapping table I used is available at GoogleDrive enter link description here
I didn’t convert all data from echocardiography, but specific data that have clinical importance (such as ejection fraction, E/A, etc.).

I want to convert other kinds of data such as pulmonary function test or ECG.
Is there anybody who has experience for these job?


Laboratory measurement 외의 데이터 변환: 심초음파 데이터 변환
(Anna Ostropolets) #2

@SCYou
Do you have a file with the data you want to map?


(Manlik Kwong) #3

Hi Seng,

I am forming a vocabulary to cover Electrocardiographic (ECG) data originating from pre-hospital (Emergency Medical Services) and in-hospital sources - from electrocardiographs, 12-lead capable defibrillators, and ECG management systems covering the top device and ECG management systems. The ECG vocabulary would cover mapping of ECG lead level measurements and unconfirmed/confirmed diagnosis findings to standard OMOP concepts where possible and original source vocabularies organized by individual vendor and/or programs.

The purpose is to provide OMOP support for medical device based cohort discovery to augment and supplement EHR based cohort discovery.

What are you thinking in this context?

  • MK

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Tufts Medical Center Boston MA

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Tufts Clinical and Translational Science Institute
Tufts Medical Center Boston MA

E-mail: mkwong@mailto:mkwong2155@gmail.comtuftsmedicalcenter.org

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(Seng Chan You) #4

Thank you @aostropolets , @mkwong

My next target database is also ECG.
My institution open the free accessible ECG database (ECG-ViEW II, you can see the paper [here][1])

So, I need concept ids for ‘PR interval’, ‘RR interval’, "QRS interval’, ‘QT interval’, ‘QTc interval’, ‘P wave axis’, ‘QRS axis’, 'T wave axis.

Thank you again for your interest and comments!
[1]: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0176222


(Manlik Kwong) #5

Hi Seng,

For lead measurements - at least the basic ones like “Global” and lead specific - there are LOINC based concepts in the standard OMOP vocabularies. Some measurements programs like those from Physio-Control have the basics, while those from Philips TC50/70 for example have more extensive global and lead measurements available - so you will need to have both a custom and “standard” mappings - at least that is how I’m handling this for GE12SL, Philips, and GLASGOW based electrocardiographs and defibrillators.

Then there is the concept mapping of the 12-lead Interpretation statements, modifiers, and qualifiers - again dominated by GE12SL, Philips 0B, and GLASGOW. On top of that - I assume you would be mostly interested in confirmed 12-lead ECGs (vs unconfirmed) - which means you will have place holders for over-read cardiologist free text entries, edits, and deletions if you really want to dig into cardiologist overread accuracy, or initial findings, etc.

I’m hoping to have a proposed vocabulary posted to OHDSI by the end of the year to cover the above commercial measurements and criteria - including my own. Let me know what ECG devices and management system you are using - I may already have an OMOP mapping and software worked out.

Best - MK


Concept for ECG reading of QTc interval
(Christian Reich) #6

@mkwong, @SCYou and friends:

So, we have LOINC, we have @SCYou’s lists. What’s next? Should this be a set of conventions with preferred/predefined vocabulary entries like for smoking? Where are we going with this?


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