OMOP Odyssey - InterSystems OMOP, The Cloud Service (Troy)

Welcome to the start of the OMOP Odyssey. Our goal is to bridge the gap between clinical data (often in FHIR format) and the analytical power of the OMOP Common Data Model (CDM). We’ll be using the InterSystems OMOP Cloud Service as our primary vessel for this transformation.

The Objective: Troy

In this first stage, we need to establish our destination: a functional OMOP CDM 5.4 database. We’ll be using an external PostgreSQL instance to host our CDM, and we’ll configure the InterSystems service to target it.

Architecture Overview

Provisioning the External Database

We’re starting with a fresh PostgreSQL instance on AWS RDS. Our first task is to create the schema and tables required for OMOP CDM 5.4.

AWS RDS Provisioning

Setting up the Environment

We’ll use R and the DatabaseConnector and SqlRender libraries from the OHDSI community to execute the DDL (Data Definition Language) for the CDM.

R Environment Setup

# R Snippet for OHDSI libraries
install.packages("DatabaseConnector")
install.packages("SqlRender")
Sys.setenv("DATABASECONNECTOR_JAR_FOLDER" = "/home/sween/Desktop/OMOP/iris-omop-extdb/jars")
library(DatabaseConnector)
downloadJdbcDrivers("postgresql")

Downloading Drivers

Executing the DDL

With our drivers in place, we connect to the PostgreSQL instance and execute the DDL to create the OMOP tables.

Connecting to Postgres

# Connect and Create
cd <- DatabaseConnector::createConnectionDetails(
  dbms = "postgresql",
  server = "extrdp-ops.biggie-smalls.us-east-2.rds.amazonaws.com/OMOPCDM54",
  user = "postgres",
  password = "REDACTED",
  pathToDriver = "./jars"
)

CommonDataModel::executeDdl(
  connectionDetails = cd,
  cdmVersion = "5.4",
  cdmDatabaseSchema = "omopcdm54"
)

Executing DDL Progress

Verifying the Work

Now let’s check our work. We should have an external PostgreSQL OMOP database ready to receive data.

Verifying OMOP Tables

Configuring the InterSystems OMOP Cloud Service

Finally, we configure the InterSystems OMOP Cloud Service to point to our newly created destination. This completes the transformation pipeline from FHIR to our external OMOP database.

Cloud Service Configuration

The InterSystems OMOP Cloud Service is now all set! The journey has just begun…

Stage Troy Complete

Stay tuned as we continue the OMOP Odyssey.