Carrot ETL End-to-End Workflow Documentation

Carrot ETL End-to-End Workflow Documentation

This guide walks you through the complete Carrot ETL workflow using sample healthcare data. You’ll transform patient records, visits, diagnoses, medications, and procedures into the OMOP Common Data Model format.

What this ETL Workflow helps you accomplish

By the end of this guide, you’ll have:

  • Profiled sample healthcare data using WhiteRabbit
  • Created data mappings using Carrot Mapper
  • Executed the transformation using Carrot Transform
  • Generated OMOP CDM-compliant data ready for research

Sample Data Overview

The sample data package contains everything you need to complete this workflow:

  • WhiteRabbit_sample_input_csv/ - Folder containing sample CSV file for Phase 1 (WhiteRabbit profiling)
    • patients.csv - Patient demographics and contact information
  • Carrot_Mapper_input_Sample_files/ - Folder containing sample files for Phase 2 (Carrot Mapper)
    • sample-scanReport.xlsx - Sample scan report
  • CarrotTransform_input_sample_files/ - Folder containing sample files for Phase 3 (Carrot Transform)
    • Rules - Awesome Test - 51 - V1 - 2025-12-02 16_27_07.581623.json - Sample mapping rules in JSON V1 format
    • Rules - Awesome Test - 51 - V2 - 2025-12-02 16_47_32.099475.json - Sample mapping rules in JSON V2 format
    • Rules - Rules - Awesome Test - 51 - 2025-12-02 20_52_37.060901.csv - Sample mapping rules in CSV format

Download sample data files →

Prerequisites

  • macOS, Linux, or Windows system
  • Java 8 or higher installed
  • WhiteRabbit v1.0.0 or later
  • Access to Carrot Mapper platform
  • Python 3.10+

Data Profiling with WhiteRabbit

Use WhiteRabbit to analyse the sample data and generate a scan report. This phase helps you understand the data structure and quality before transformation.

WhiteRabbit

Data Transformation with Carrot Mapper

Configure field mappings and transformation rules using Carrot Mapper. This phase defines how the sample data will be converted to OMOP CDM format.

Carrot Mapper

Data Execution and Validation

Execute the transformation using Carrot Transform and validate the results. This phase performs the actual data conversion and ensures quality standards are met.

Carrot Transform

Getting Started

  1. Download the sample data files to your local machine
  2. Follow each phase in order - each builds on the previous one
  3. Use the same sample data throughout the workflow for consistency

Additional Resources

Ready to begin? Start with Phase 1: Data Profiling with WhiteRabbit to begin your ETL workflow.

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