OMOP_CDM_TABLES : GENERATING A NEW ADAPTED CDM

This project contains several components to create and test a new and adaptable Common Data Model (CDM) based on the OMOP CDM standard.

Directory Structure

CDMS

This directory contains common data models that can be used as a basis for creating a new and adaptable CDM.

ENOMIA_CSV_TABLES

This directory includes all standard tables of the OMOP CDM, made available through the eunomia package for R software.

MOCK_DATA

This directory holds mock data for testing the insertion and functionality of the newly created tables.

NEW_CDM

This directory is where the output of the new adapted common data model is stored.

Scripts

script_table_creation.R

This script is used to create new tables as per the OMOP CDM standard.

script_inserting_data.R

This script inserts mock data to test the functionality of the tables.

script_generating_a_new_cdm.R

This script generates the new adapted CDM using the DatabaseConnector and dplyr libraries.

script_some_charts.R

This script generates some charts from the mock data to briefly test the quality of the tables.

Getting Started

Prerequisites

• R
• DatabaseConnector package
• dplyr package
• eunomia package

Running the Scripts

1. Use script_table_creation.R to create new tables according to the OMOP CDM standard.
2. Use script_inserting_data.R to insert mock data and test table functionalities.
3. Use script_generating_a_new_cdm.R to create the new adapted CDM.
4. Use script_some_charts.R to generate charts and test the quality of the tables.

License

This project is licensed under the MIT License.

Acknowledgments

• OMOP CDM
• eunomia package
• DatabaseConnector package
• dplyr package
• oxford-pharmacoepi/PETDiagnostics package

References

https://github.com/OHDSI/Eunomia
https://github.com/oxford-pharmacoepi/PETDiagnostics