Import a Single Value Set

Introduction

This use case will walk through the process of downloading a value set from VSAC, using the vsac-to-ohdsi tools to extract, and convert the value set into a format that can be imported into OHDSI, and using the OHDSI Atlas tool to import the value set into OHDSI. This use case will then show how to create a cohort (phenotype) using the imported value set. For this use case a UMLS license is required for full access to VSAC. Instructions for getting a UMLS license are here.

Download a Value Set from VSAC

Note: We will need to download the value set as text. Sometimes this option is not available when download is selected. Logging off and retrying the download or logging off, logging back on, and then retrying the download usually enables this functionality.

Navigate to the VSAC Search Page.
  • Select the “Search Value Sets” tab.
  • Enter “covid vaccination” into the Query field.
  • Select Search.
  • Select the COVID_19Vaccine_CVX value set from the list of values.
  • Select Download.
  • Select Text as the download type in the pick list that appears.



The value set should now be downloaded as a single .txt.zip file as shown below. This is the file that will be used to create the value set in OHDSI.

Note: The value set used in this example (COVID_19Vaccine_CVX) is not suitable for production. This value set is missing a large number of codes that should be included when looking for covid vaccination codes.

More on how to evaluate and find suitable value sets can be found on the Getting Started with VSAC Value Sets which can be found under the “Getting Started” menu at the top of this page.