Choosing the right data model is never a trivial task. In the biomedical data space there are tons of proprietary and open models available: one could create a custom format or work with a widely adopted industry standard. Whatever choice is made, one always has to deal with versioning and consider integration with other formats and systems used within the specific data ecosystem. We at The Hyve help our clients make the right choice by evaluating fit for purpose based on the analysis use cases and develop data harmonization strategies. When needed, we also create ad hoc adaptations or newer versions of the data models. A standard we advocate and specialise in is the OMOP / OHDSI Common Data Model. In this article we will focus on comparing OMOP CDM version 5.3.1against CDM version 6.0. This comparison should help you answer the question which version would work best in your data landscape.
Before we dive into a version comparison, let’s start with a short history of the OMOP CDM.
The Observational Medical Outcomes Partnership Common Data Model, aka OMOP CDM, aims to harmonize disparate coding systems with minimal information loss to a standardized vocabulary.
To quote Patrick Ryan, leader of the OHDSI community: “OMOP was initially formed in 2008. The majority of the effort in the initial months was designing the series of methodological experiments. There was discussion on the need to bring together a community of disparate databases and to test a centralized model and distributed network approach, but the specific details of what the CDM would look like to enable that research didn’t come out until 2009.”
If you are completely new to the OMOP / OHDSI community, we recommend reading these first:
If you are familiar with the OMOP CDM, you may have worked with version 5. Subversion v5.3.1 is the latest and is supported by all the recent OHDSI tooling. To each subversion, the community added new tables (e.g. cost, visit_detail) and new fields (e.g. condition_status, admitting_source). All the details of added features can be found in the release notes.
To the most recent version, v6.0, a number of groundbreaking changes were made, most notably the removal of the death table. It was released in October 2018.
Which version of the OMOP CDM researchers are choosing highly depends on their use cases or research questions. One major advantage of CDM v5.3.1 over v6.0 is that it is supported by all analysis tools (Achilles, Atlas, etc.). Therefore, if the aim of converting your data to OMOP is to use the OHDSI tools you are better off with v5.3.1.
However, as the community grows and there are more use cases to work with the need emerged for some changes. This is exactly what CDM version v6.0 takes into consideration. It provides a very good model for fitting all use cases together.