The goal of this project is to ease running OHDSI projects in Azure.
Some of the OHDSI projects include:
- Common Data Model (CDM), including Vocabulary
- Atlas - OSS tool used to conduct analyses on standardized observational data converted to the OMOP Common Data Model V5
- WebApi - contains all OHDSI RESTful services that can be called from OHDSI applications
- Achilles - provides descriptive statistics on an OMOP CDM database
- ETL-Synthea - Conversion from Synthea CSV to OMOP CDM
You can use Azure DevOps pipelines to manage your environment, see the guide for creating your environment for an overview.
Your administrator can manage Azure Resources in your bootstrap resource group and your Azure DevOps setup using Terraform. You will also need to work with your Azure administrator to setup your Azure DevOps using the administrative steps.
The Azure resources in the OMOP resource group are managed through Terraform.
You can host your CDM in Azure SQL. You can load your vocabularies into Azure Storage so that the Azure DevOps Vocabulary Release Pipeline can populate your Azure SQL CDM.
You can setup Atlas and Webapi using the Broadsea Build Pipeline to build and push the Broadsea webtools (for Atlas / WebApi) image into Azure Container Registry. You can then run the Broadsea Release Pipeline to configure Atlas and WebApi in your Azure App Service.
You can also setup Achilles and Synthea using the Broadsea Build Pipeline to build and push the Broadsea Methods (for Achilles and Synthea) image into Azure Container Registry. You can then run the Broadsea Release Pipeline to perform the following steps:
- Run an ETL job and use Synthea to generate synthetic patient data as an optional step
- Run Achilles to characterize the CDM data in Azure SQL
OHDSI.on.Azure.-.E2E.Overview.with.narration.mp4
This setup supports a modified version of the CDM v5.3.1 schema based on the CDM v5.3.1 for SQL Server.
You can review more notes on the modifications in the readme.
To get started, first clone the repository.
git clone https://github.com/microsoft/OHDSIonAzureYou can work through the notes on creating your environment quickstart which will walk through how to set up OHDSI on Azure.
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