ielis / ETL-Synthea

Conversion from Synthea CSV to OMOP CDM

Utility to Load Synthea CSV data to OMOP CDM

Currently supports CDM v6.0 (see branch v5.3.1-updates for CDM v5.3 support)

Follow the steps on the synthea wiki to run the program and generate the files. This builder works off of the csv files, not the fhir files. To do this the exporter.csv.export option in the ./src/main/resources/synthea.properties file needs to be set to TRUE.

Step by Step Example (R package)

 devtools::install_github("OHDSI/ETL-Synthea")

 library(ETLSyntheaBuilder)

 # We are loading into a local PostgreSQL database called "synthea10".  
 # The schema to load the Synthea tables is "native".
 # The schema to load the Vocabulary and CDM tables is "cdm_synthea10".  
 # The username and pw are "postgres" and "lollipop".
 # The Synthea and Vocabulary CSV files are located in /tmp/synthea/output/csv and /tmp/Vocabulary_20181119, respectively.
 
 cd <- DatabaseConnector::createConnectionDetails(
  dbms     = "postgresql", 
  server   = "localhost/synthea10", 
  user     = "postgres", 
  password = "lollipop", 
  port     = 5432
)

ETLSyntheaBuilder::DropVocabTables(connectionDetails = cd,
                                   cdmDatabaseSchema = "cdm_synthea10")

ETLSyntheaBuilder::DropEventTables(connectionDetails = cd,
                                   cdmDatabaseSchema = "cdm_synthea10")
                                   
ETLSyntheaBuilder::DropSyntheaTables(connectionDetails = cd, 
                                     syntheaDatabaseSchema = "native")
                                     
ETLSyntheaBuilder::DropMapAndRollupTables (connectionDetails = cd, 
                                           cdmDatabaseSchema = "cdm_synthea10")
                                           
ETLSyntheaBuilder::CreateVocabTables(connectionDetails = cd, 
                                     vocabDatabaseSchema = "cdm_synthea10")
                                     
ETLSyntheaBuilder::CreateEventTables(connectionDetails = cd, 
                                     cdmDatabaseSchema = "cdm_synthea10")
                                     
ETLSyntheaBuilder::CreateSyntheaTables(connectionDetails = cd, 
                                       syntheaDatabaseSchema = "native")
                                       
ETLSyntheaBuilder::LoadSyntheaTables(connectionDetails = cd, 
                                     syntheaDatabaseSchema = "native", 
                                     syntheaFileLoc = "/tmp/synthea/output/csv")
                                     
ETLSyntheaBuilder::LoadVocabFromCsv(connectionDetails = cd, 
                                    vocabDatabaseSchema = "cdm_synthea10", 
                                    vocabFileLoc = "/tmp/Vocabulary_20181119")
                                    
ETLSyntheaBuilder::CreateVocabMapTables(connectionDetails = cd, 
                                        cdmDatabaseSchema = "cdm_synthea10")
                                        
ETLSyntheaBuilder::CreateVisitRollupTables(connectionDetails = cd, 
                                           cdmDatabaseSchema = "cdm_synthea10", 
                                           syntheaDatabaseSchema = "native")

ETLSyntheaBuilder::LoadEventTables(connectionDetails = cd, 
                                   cdmDatabaseSchema = "cdm_synthea10", 
                                   syntheaDatabaseSchema = "native")

Simulating Data with Synthea

For commented code used to convert the Synthea data see extras/codeToRun.R

For more information on Synthea visit: https://synthetichealth.github.io/synthea/

Get Synthea from GitHub: https://github.com/synthetichealth/synthea