Downloading the OMOP Terminology Tables Data

The OMOP terminology tables include the vocabulary, concept, concept_ancestor, etc. tables that define the terminologies used by your OMOP instance. These tables can be populated from files that are downloaded from OHDSI Athena. Before you can download the files you'll need to get an account if you don't already have one.

Download Terminology Data from Athena

After Loging into Athena, go to the Download page by selecting Download option in the upper right hand corner of the screen. The terminologies used as part of a basic standard install are selected. The fhir-to-omop tools were built using the preselected tables with the addition of the following two terminologies.


After submitting the request for the download you will receive an email with instructions on how to download the vocabulary package you've created. You can also retrieve the vocabulary package you just created as well as other packages you've created from the Download History Page


When creation of the terminology package has completed you will receive an email that includes a list of the terminologies you've requested as well as instructions on how to finish the process. This email will look something like what is shown below. Click here to see the full email example.


Click on the download "link" towards the bottom of the email.


This should download a zip file to your localhost. Move this file to the location where you would like to store these files. This can be any directory (there is a configuration setting that points to the directory where you keep these files). Unzip the zip file.


After unzipping the files shown below should be in the unzipped folder.


We now need to import the CPT4 vocabulary by running the cpt.bat file using the instructions in the readme.txt file. Open a cmd prompt. Navigate to the folder that contains the vocabulary files. Run cpt.bat <MY_API_KEY>. This will download the CPT4 data from the interwebs so an interwebs connection is required. This step takes several minutes to complete (you can see from the timestamp that it took about 25 minutes for me). Now would be a good time to go get a cup of coffee and a breath of fresh air. When the process finishes you should see something like the following.