The EHDEN Academy, in collaboration with our guest lecturer, Maxim Moinat, Data Engineer/ OHDSI-OMOP expert, The Hyve, is pleased to announce the launch of our next course: Introduction to Usagi & Code Mappings for an ETL. The Academy is free, used in more than 60 countries, and only requires a participant to set up an account and log in.
This six-chapter course, our fifteenth, demonstrates how to work with the Usagi tool, which helps in the process of mapping codes from a source system into the standard terminologies stored in the OMOP CDM. Upon completion of the course, you will be able to import your codes into Usagi, review and export the code mappings for use in your ETL pipeline. It also covers more advanced features of Usagi that will make the code mapping process easier, like filtering, auto concept id column, concept information and mapping types.
"Mapping medical coding systems can be a big effort during the OMOP CDM harmonisation process. Usagi was developed to support this process and knowing how to most efficiently use it can save a lot of time. Most importantly, the Usagi module joins the others in our OMOP common data model ETL learning pathway, further enhancing this unique training resource for anyone wishing to map source data to the CDM in a rigorous and reproducible manner,” said Maxim Monat.
“We are delighted to add this new Usagi course to the EHDEN Academy, also further strengthening the training resource we have that is fundamental to the implementation of the OMOP common data model. To date, we have used this learning pathway to train almost 50 SMEs in EHDEN, will be adding twenty more this year from our last SME call, and have seen colleagues worldwide using these training modules. We are also indebted to colleagues like Maxim, who have volunteered their time to create high quality content,” said Nigel Hughes, Scientific Director, Epidemiology, Global R&D, Janssen (Co-Lead EHDEN).
Chapters 1 & 2 begin with an introduction to Usagi, which includes a recap of the OMOP vocabularies and provides the context of why and when to use Usagi. It then covers the setting up of Usagi following three steps: (downloading the OMOP vocabulary; building the Usagi vocabulary index; portable index).
Chapter 3 explains how to import code into Usagi. With this step complete, chapter 4 presents the best matching target concepts based on string similarity. Chapter 5 addresses source to concept mapping and loading STCM in the OMOP CDM.
The final chapter 6 takes a look and some of Usagi’s more advanced features such as Concept detail, Athena and Web Search, Invalid target concepts, and Multi-add/replace/deletion of a target concept.
As of the time of this course launch, SMEs who have used the ETL learning pathway are mapping more than 500 million anonymous health records to the OMOP common data model in collaboration with Data Partners in twenty-six European countries.
We hope many more of you will also find this course beneficial and will add this to your existing portfolio of EHDEN Academy courses, or if new, add more to this one. You can enrol on the Academy via this link.
Please keep an eye out for new courses we will be adding throughout this year: