SDC-CDM

A Structured Data Capture Common Data Model (SDC-CDM) for the SDC Implementation Guide (SDC IG).

Purpose

The SDC-CDM is designed to streamline the management of SDC processes by providing a unified data model for SDC data.

Example Use Cases

• Data Integration: Add support for SDC data into a new or existing database by adopting a single, consistent schema.
• Unified Reporting and Analytics: Be able to use the same SQL queries to generate reports and perform data analytics between any database that has adopted the schema.
• Data Import/Export: Import and export various SDC data types for interoperability with other systems.
• Development and Testing: Use the provided .NET library and Jupyter-style notebooks to develop, test, and validate the CDM schema.

This Repository

The SDC-CDM GitHub repository hosts the following projects to help users and developers work with the SDC-CDM

• database/ - A standardized schema to store SDC data.
• notebooks/ - Jupyter-style notebooks to onboard users and familiarize themselves with the CDM.
• SdcCdmLib/ - A .NET library serving as a reference implementation for some common operations on SDC data, including:
  • Importing SDC Forms and NAACCR V2 Messages into the CDM
  • Exporting data from the CDM into FHIR CPDS Bundles
• sample_data/ - Sample data for testing and demonstration purposes.

Getting Started

Notebook

The notebooks contain a number of examples of how to use the CDM schema.

.NET Polyglot Notebook

1. Open the Notebook: Open notebooks/try_sdc_cdm_dotnet.dib using VS Code with the Polyglot Notebooks extension installed.

2. Notebook Walkthrough: The notebook will guide you through:

   • Creating a SQLite database loaded with the CDM schema.
   • Importing SDC templates, SDC forms, and NAACCR V2 messages.
   • Exporting CDM data into FHIR CPDS bundles.

Python Jupyter Notebook

1. Open the Notebook: Open notebooks/try_sdc_cdm_python.ipynb using a Jupyter notebook viewer.

2. Notebook Walkthrough: The notebook will guide you through:

   • Creating a SQLite database loaded with the CDM schema.
   • Importing SDC templates, SDC forms, and NAACCR V2 messages.

Library

We maintain a .NET library at SdcCdmLib/ that provides reference implementations for various import and export operations related to SDC data. For example usage, refer to the Polyglot Notebook located in the notebooks/ directory.

Standalone Database

A docker compose file is provided under database/ to set up a PostgreSQL database containing the CDM schema.

1. Copy Environment Variables:

   cp .env.example .env
   

   The default values will work for initial setup. Docker Compose will automatically use any .env file in the current working directory

2. Start Docker Compose:

   docker compose up
   

   This command initializes a PostgreSQL database and loads the OMOP CDM schema on the first run.

3. Resetting the Database: To reset the database, execute:

   docker compose down -v
   

   This command removes the persistent database volume (with the -v flag). Afterward, you can restart the database with:

   docker compose up