OHDSI Hades Image

Docker image for running OHDSI Hades tools in a container

Contents

• This Image
• DatabaseConnector
• Synthea ETL
• Achilles
• DataQualityDashboard

This Image

Building

docker build --tag hades:latest .

Running a Container

docker run --name hades --volume `pwd`/home:/home/ohdsi --env TZ --env OMOP_SERVER --env OMOP_USER --env OMOP_PASSWORD --interactive --tty --rm hades:latest

This runs an R REPL with DatabaseConnector and some database drivers pre-loaded. The OHDSI/Hades tools mentioned in this document are pre-installed.

DatabaseConnector

See the DatabaseConnector package for details on settings the connection details for your database. The drivers for sql server, postgresql and sqlite have been pre-loaded in this image.

cd <- DatabaseConnector::createConnectionDetails(
  dbms          = "sql server",
  server        = "server;Database=db",
  user          = "user",
  password      = "password",
  extraSettings = "encrypt=true;trustServerCertificate=true;"
)

ETLSyntheaBuilder

• package website
• get vocab from Athena
• generate synthetic population

example

java -jar synthea-with-dependencies.jar --exporter.csv.export=true --exporter.fhir.export=false -p 1000 Ohio Cincinnati

library(ETLSyntheaBuilder)

cdmVersion     <- "5.4"
syntheaVersion <- "3.3.0"
cdmSchema      <- "cdm"
syntheaSchema  <- "synthea"
syntheaFileLoc <- "/home/ohdsi/synthea"
vocabFileLoc   <- "/home/ohdsi/vocab"

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

Achilles

Automated Characterization of Health Information at Large-Scale Longitudinal Evidence Systems (ACHILLES) Achilles provides descriptive statistics on an OMOP CDM database. ACHILLES currently supports CDM version 5.3 and 5.4.

• Code Repository
• Package Site

run Achilles

library(Achilles)

Achilles::achilles(
  cdmVersion = "5.4",
  connectionDetails = cd,
  cdmDatabaseSchema = "cdm",
  resultsDatabaseSchema = "achilles"
)

The cdmDatabaseSchema parameter, and resultsDatabaseSchema parameter, are the fully qualified names of the schemas holding the CDM data, and targeted for result writing, respectively.

DataQualityDashboard

• package website

cdmDatabaseSchema <- "cdm" # the fully qualified database schema name of the CDM
resultsDatabaseSchema <- "dqd" # the fully qualified database schema name of the results schema (that you can write to)
cdmSourceName <- "Synthea synthetic health database" # a human readable name for your CDM source
cdmVersion <- "5.4" # the CDM version you are targetting. Currently supports 5.2, 5.3, and 5.4
outputFolder <- "output"
outputFile <- "results.json"

# run the job --------------------------------------------------------------------------------------
DataQualityDashboard::executeDqChecks(
  connectionDetails = cd,
  cdmDatabaseSchema = cdmDatabaseSchema,
  resultsDatabaseSchema = resultsDatabaseSchema,
  cdmSourceName = cdmSourceName,
  cdmVersion = cdmVersion,
  outputFolder = outputFolder,
  outputFile = outputFile)

References

• Hades
• OMOP Common Data Model