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How to create a Synthetic OMOP CDM

Overview

The purpose of this document is to guide you through the process of creating a synthetic OMOP CDM database.

Follow these steps

  • Install Java Open JDK from bellsoft (Liberica JDK) Download OpenJDK builds of Liberica JDK, Java 8, 11, 17, 19 | BellSoft Java (bell-sw.com)

    • Set JAVA_HOME to C:\Program Files\BellSoft\LibericaJDK-17\
    • Add C:\Program Files\BellSoft\LibericaJDK-17\bin\ to PATH
    • Make sure you've got the following version by running java -version:
    openjdk version "17.0.6" 2023-01-17 LTS
OpenJDK Runtime Environment (build 17.0.6+10-LTS)
OpenJDK 64-Bit Server VM (build 17.0.6+10-LTS, mixed mode, sharing)

  • Download Synthea v3.0.0 https://github.com/synthetichealth/synthea/releases/tag/v3.0.0

  • Create config file named synthea-settings.conf with the following content:

    exporter.csv.export = true
exporter.json.export = false
exporter.fhir.export = false
exporter.fhir.transaction_bundle = false
exporter.hospital.fhir.export = false
exporter.practitioner.fhir.export = false
exporter.baseDirectory = ./output
exporter.encoding = UTF-8

  • Run Synthea from command line:

java -jar synthea-with-dependencies.jar -p <num of patients> -c synthea-settings.conf

  • Download vocabularies from Athena - https://athena.ohdsi.org/, you'll need to register first, choose "LOINC", "RxNorm" as vocabs version 5.x. When the files are ready you will get an email with a link to download a compressed file which weights about ~850MB

  • Create PostgreSQL Database

  • Create 4 schemas with correct permissions to your db user (cdm, cdm_results, native and temp)

    CREATE SCHEMA IF NOT EXISTS cdm
    AUTHORIZATION postgres_admin;
GRANT USAGE ON SCHEMA cdm TO ohdsi_admin;
GRANT USAGE ON SCHEMA cdm TO ohdsi_app;
GRANT ALL ON SCHEMA cdm TO postgres_admin;


CREATE SCHEMA IF NOT EXISTS native
    AUTHORIZATION postgres_admin;
GRANT ALL ON SCHEMA native TO postgres_admin;

CREATE SCHEMA IF NOT EXISTS cdm_results
    AUTHORIZATION postgres_admin;
GRANT USAGE ON SCHEMA cdm_results TO ohdsi_admin;
GRANT USAGE ON SCHEMA cdm_results TO ohdsi_app;
GRANT ALL ON SCHEMA cdm_results TO postgres_admin;


CREATE SCHEMA IF NOT EXISTS temp
    AUTHORIZATION postgres_admin;
GRANT ALL ON SCHEMA temp TO postgres_admin;

  • Install RStudio and Hades packages or run Broadsea with docker-compose and enable basic authentication.

  • Install ETL-Synthea and Achilles OHDSI R packages by running the following script inside RStudio

    install.packages("devtools")
install.packages("remotes")

  • Restart R session

  • Download PostgreSQL jdbc driver

    DatabaseConnector::downloadJdbcDrivers(
    'postgresql',
    pathToDriver = 'jdbcdrivers',
    method = "auto")

  • Configure and run the following script

    connectionDetails <- DatabaseConnector::createConnectionDetails(
    dbms            = "postgresql",
    server          = "your_postresql_server/db_name",
    user            = "postgres",
    password        = "mypass",
    port            = 5432,  
    pathToDriver    = "jdbcdrivers"
)

cdmVersion        <- "5.4"
cdmDatabaseSchema <- "cdm"
syntheaSchema     <- "native"
syntheaFileLoc    <- "synthea/10person"
vocabFileLoc      <- "/vocab/vocabulary"
syntheaVersion    <- "3.0.0"

# Create CDM tables
ETLSyntheaBuilder::CreateCDMTables(connectionDetails,cdmDatabaseSchema,cdmVersion)
# Create synthea tables
ETLSyntheaBuilder::CreateSyntheaTables(connectionDetails,syntheaSchema, syntheaVersion)
# Populate synthea tables
ETLSyntheaBuilder::LoadSyntheaTables(connectionDetails,syntheaSchema,syntheaFileLoc)
# Populate vocabulary tables
ETLSyntheaBuilder::LoadVocabFromCsv(connectionDetails,cdmDatabaseSchema,vocabFileLoc)
# Populate event tables
ETLSyntheaBuilder::LoadEventTables(connectionDetails,cdmDatabaseSchema,syntheaSchema,cdmVersion,syntheaVersion)

library(Achilles)

achillesResults <- Achilles::achilles(
    connectionDetails       = connectionDetails, 
    cdmDatabaseSchema       = "cdm", 
    resultsDatabaseSchema   = "cdm_results",
    vocabDatabaseSchema     = "cdm",         
    scratchDatabaseSchema   = "temp",
    numThreads              = 1,
    cdmVersion              = "5.4", 
    outputFolder            = "output",
    optimizeAtlasCache      = TRUE)

  • Generate DDL scripts using OHDSI WebAPI website by posting to:

http://<server:port>/WebAPI/ddl/results?dialect=postresql&schema=cdm_results&vocabSchema=cdm&tempSchema=temp&initConceptHierarchy=true

for more info see https://github.com/OHDSI/WebAPI/wiki/CDM-Configuration#results-schema-setup.

  • Save and run the generated SQL statements using pgAdmin.

  • Add you new OMOP CDM Source to Atlas.