INTRODUCTION AND PURPOSE
This document is designed to outline the procedure for downloading the latest version of the vocabulary for all HPOs via a GCS bucket.
SCOPE
The process applies to all program partner organizations responsible for sharing participant data (e.g., EHR) with the DRC. All vocabulary can be downloaded from a GCS bucket.
PROCEDURES
KEYWORDS
- SOP: Standard Operating Procedure
- DRC: Data and Research Center
- Data Steward: Individual responsible for uploading EHR data
RESPONSIBILITY
An organization’s designated Data Steward(s) is/are responsible for adherence to this procedure.
PROCESS
Assumptions:
- Each site’s Data Steward has a registered account
Step 1 - Access to vocabulary-updates bucket
Data Stewards should make sure that they have a valid PMI-Ops account. If not, contact the AoU Sysadmin Team at drcsupport@vumc.org to request or unlock your account.
Step 2 - Download the Vocabulary Collection in GCS
After authenticating with your PMI-ops account, you can download the AoU bundled vocabularies inside the GCS bucket by accessing the bucket named vocabulary-updates using gsutil by:
- Open Google Cloud SDK shell
- Authenticate: Enter gcloud auth login
- This opens a browser window to authenticate the Google Cloud Platform.
- Login using the assigned pmi-ops account (e.g. john.smith@pmi-ops.org)
- Copy files to a local folder:
| gsutil -m cp -r gs://vocabulary-updates/* c:\local_folder_name |
Step 3 - Loading the Vocabulary
Click on this reference describing how to load the vocabulary for different databases: https://github.com/OHDSI/CommonDataModel?files=1. After you click on the database you use, click the “VocabImport” link for further instructions. Here is the script to load the common data model, version 5.0 vocabulary tables for SQL Server database:https://github.com/OHDSI/CommonDataModel/tree/v5-historical/Sql%20Server/VocabImport
*You do NOT need to run a script to merge the CPT4 codes with the concept.csv.
**To ensure that you downloaded the correct version of the vocabulary, check the vocabulary file to verify that it is this version: v5.0 27-FEB-26.
Sample:
cat VOCABULARY.csv | grep None
None OMOP Standardized Vocabularies OMOP generated v5.0 27-FEB-26. 44819096
OR Run SQL Query on your vocabulary table:
SELECT * FROM vocabulary
WHERE vocabulary_id = 'None'
ISSUE REPORTING
Report any issues with downloading the vocabulary to support@aou-ehr-ops.zendesk.com. A member of the DRC team will contact the Data Steward to assist with resolving the issue. For issues with your PMI-Ops account, please get in touch with drcsupport@vumc.org.
REFERENCES
APPENDIX
If you are experiencing severe technical difficulties concerning downloading the vocabulary using the command line, you may consider using the following web interface link:
https://console.cloud.google.com/storage/browser/vocabulary-updates
Please note that the above link should serve as a last resort as this method is less optimized and configurable.