Radiotherapy Data Integration into OMOP CDM

Project Overview

This project aims to extend the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) to incorporate radiotherapy (RT) data from DICOM files. The goal is to standardize RT data representation within the OMOP framework, facilitating large-scale analysis and research in radiation oncology.

Current State

We have developed a Python script that serves as a foundation for extracting RT data from DICOM files and structuring it in a format compatible with our proposed OMOP CDM extension. The script currently:

Reads DICOM files (including RT-specific files like RTPLAN, RTSTRUCT, and RTDOSE)
Extracts relevant information into two main structures: rt_occurrences and rt_features
Converts these structures into pandas DataFrames
Optionally saves the results to CSV files

Project Structure

/
├── DICOM.py              # Main Python script for DICOM processing
├── requirements.txt      # Python dependencies
├── sample_output/        # Directory containing sample output CSV files
└── README.md             # This file

How to Use

Ensure you have Python 3.7+ installed.
Install required packages:
```
pip install -r requirements.txt
```
Update the directory variable in DICOM.py to point to your DICOM files.
Run the script:
```
python DICOM.py
```

Current Limitations

The full range of RT-specific data is not captured, especially for complex objects like RTPLAN and RTSTRUCT.
Data is not loaded into an actual OMOP CDM database structure.

Next Steps

Enhance data extraction for all RT modalities
Develop OMOP concept mapping for RT-specific data
Implement integration with existing OMOP tables
Extend OMOP vocabulary for RT concepts
Develop database integration for inserting data into OMOP CDM structure
Implement data validation and error handling
Create comprehensive documentation and testing suite

Contributing

This project is part of a collaborative effort to standardize RT data within the OMOP framework.

Erfandarzi/OMOP