Skip to content

Latest commit

 

History

History
67 lines (47 loc) · 3.37 KB

README.md

File metadata and controls

67 lines (47 loc) · 3.37 KB
Raw

Utility to Load Synthea CSV data to OMOP CDM

Currently supports CDM v5.3 and v5.4

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

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

 library(ETLSyntheaBuilder)

 # We are loading a version 5.4 CDM into a local PostgreSQL database called "synthea10".
 # The ETLSyntheaBuilder package leverages the OHDSI/CommonDataModel package for CDM creation.
 # Valid CDM versions are determined by executing CommonDataModel::listSupportedVersions().
 # The strings representing supported CDM versions are currently "5.3" and "5.4". 
 # The Synthea version we use in this example is 2.7.0.
 # However, at this time we also support 3.0.0, 3.1.0, 3.2.0 and 3.3.0.
 # Please note that Synthea's MASTER branch is always active and this package will be updated to support
 # future versions as possible.
 # The schema to load the Synthea tables is called "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.
 
 # For those interested in seeing the CDM changes from 5.3 to 5.4, please see: http://ohdsi.github.io/CommonDataModel/cdm54Changes.html
 
cd <- DatabaseConnector::createConnectionDetails(
  dbms     = "postgresql", 
  server   = "localhost/synthea10", 
  user     = "postgres", 
  password = "lollipop", 
  port     = 5432, 
  pathToDriver = "d:/drivers"  
)

cdmSchema      <- "cdm_synthea10"
cdmVersion     <- "5.4"
syntheaVersion <- "2.7.0"
syntheaSchema  <- "native"
syntheaFileLoc <- "/tmp/synthea/output/csv"
vocabFileLoc   <- "/tmp/Vocabulary_20181119"

ETLSyntheaBuilder::CreateCDMTables(connectionDetails = cd, cdmSchema = cdmSchema, cdmVersion = cdmVersion)
                                     
ETLSyntheaBuilder::CreateSyntheaTables(connectionDetails = cd, syntheaSchema = syntheaSchema, syntheaVersion = syntheaVersion)
                                       
ETLSyntheaBuilder::LoadSyntheaTables(connectionDetails = cd, syntheaSchema = syntheaSchema, syntheaFileLoc = syntheaFileLoc)
                                     
ETLSyntheaBuilder::LoadVocabFromCsv(connectionDetails = cd, cdmSchema = cdmSchema, vocabFileLoc = vocabFileLoc)

ETLSyntheaBuilder::CreateMapAndRollupTables(connectionDetails = cd, cdmSchema = cdmSchema, syntheaSchema = syntheaSchema, cdmVersion = cdmVersion, syntheaVersion = syntheaVersion)

## Optional Step to create extra indices
ETLSyntheaBuilder::CreateExtraIndices(connectionDetails = cd, cdmSchema = cdmSchema, syntheaSchema = syntheaSchema, syntheaVersion = syntheaVersion)
                                    
ETLSyntheaBuilder::LoadEventTables(connectionDetails = cd, cdmSchema = cdmSchema, syntheaSchema = syntheaSchema, cdmVersion = cdmVersion, syntheaVersion = syntheaVersion)

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