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Epic Clarity to OMOP -- The Spectrum Code Reboot

OMOP: The Spectrum Code Reboot

Roger Carlson • Data Analytics Engineer • Corewell Health West

The the above link on Epic UserWeb is the latest version of what has since come to be known as The Spectrum Code. We at Spectrum Health didn’t name it that. We simply found out that’s what others call it. Spectrum Health has recently been renamed to Corewell Health West, so if you want, feel free to rename it… or not.

Four years ago, we posted our first stab at pulling Epic Clarity data into OMOP here:

OMOP: Spectrum Health AoU Project.

Two years ago, we posted an expanded and extended version:

OMOP: TNG (The Next Generation)

In this latest version we’ve added more code modules and made major changes to the formatting and nomenclature of our code. Overall, is should be easier to read and implement.

How it’s organized:

  1. The code is highly modularized
  2. We differentiate first by Hospital, Ambulatory, and (in some cases) Anesthesia
  3. Next by OMOP clinical data table (visit_occurrence, measurement, location, etc.)
  4. Other divisions are possible if required by code differences (especially in measurement).
  5. Unlike previous versions, all of the code in this series are SELECT statements only.
  6. Each module will contain 3 SQL statements (pull, stage, and write), 1 or more ER diagrams, sample source_to_concept maps, and a readme file.

We hope you find them useful.

Comments and corrections greatly appreciated. Feel free to contact us with questions.

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