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ETL-CDMBuilder

Introduction

The CDM Builder can be used to transform observational datasets from their native formats and schemas into the OMOP Common Data Model (version 4).

Features

  • This builder can convert the following database:
    • Truven MarketScan Commercial Claims and Encounters (CCAE)
    • Truven MarketScan Medicare (MDCR)
    • Truven MarketScan Medicaid (MDCR)
    • OptumInsight ClinFormatics Data Mart v 5.0 (Optum)
    • Clinical Practice Research Datalink (CPRD)
    • Premier Alliance of Hospitals
    • National Health and Nutrition Examination Survey (NHANES)

Screenshot

ETL-CDMBuilder

Technology

  • The CDM Builder was created using the Microsoft .NET framework (version 4+) and is meant to be executed against Microsoft SQL Server 2012+ databases. It is only intended to run in a Windows environment.
  • Visual Studio 2011+ is required for building the solution.

System Requirements

  • SQL Server Native Client and .NET version 4+ are required on each server that will be running CDM Builder.

Dependencies

  • A SQL Server database of the OMOP Vocabulary must be accessible within your network. This will be used to map source concepts into CDM concepts.
  • In the VOCAB_ADDITIONS folder, you will need to append these files to the OMOP Vocabulary (i.e. add the SOURCE_TO_CONCEPT_MAP_JANSSEN file to the records already in SOURCE_TO_CONCEPT_MAP and do the same for the VOCABULARY table with VOCABULARY_JANSSEN).
  • In the OTHER_LOOKUPS folder, these are source lookups that do not always get delivered with raw data or need to be generated (e.g. vendor delivers as PDF and there is effort converting it into a data table).

Getting Started

There is not a executable release this version, the tool will need to be built off the source code.

  • Clone the GitHub repository locally.
  • Open the .sln file (solution) in Visual Studio.
  • Establish startup project and build the solution
  • Set the project named “org.ohdsi.cdm.presentation.buildingmanager” as the startup project. This is the GUI for the Builder.
  • Right mouse click on that project in the Solution Explorer and select the “Set As Startup Project” menu item.
  • Build the entire solution in “Release” mode.

Figure 1.0

GettingStarted

  • In the menu bar shown in Figure 1.0, toggle the “Solution Configurations” drop-down to “Release.” Then right mouse click on the whole solution in “Solution Explorer” and select the “Build” menu item.
  • Deploying the Binaries
  • As the Build process can be time- and resource-intensive, CDM Builder can be executed using multiple Windows servers. This is optional, but recommended, especially for larger databases. -The following executable is the Builder GUI that can be used on each of the Build servers: \org.ohdsi.cdm\Presentation\org.ohdsi.cdm.presentation.buildingmanager\bin\Release\org.ohdsi.cdm.presentation.buildingmanager.exe

Getting Involved

License

ETL-CDMBuilder is licensed under Apache License 2.0

Development

###Development status Beta testing, source is not set up properly to deploy an executable this release.

Acknowledgements

Janssen Pharmaceutical Research & Development, LLC