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Automatic ETL Pipeline Generation for Mapping Heterogeneous Clinical Data into the OMOP Common Data Model.

Elisabeth Mayrhuber¹, Philip Stampfer², Sai Pavan Kumar Veeranki³

¹University of Applied Sciences Upper Austria, Hagenberg, Austria.

Studies in Health Technology and Informatics

|May 12, 2026

Summary

This summary is machine-generated.

This study introduces an automated ETL pipeline to convert CSV data into the OMOP Common Data Model (CDM). This approach enhances reproducibility and maintainability for clinical research data standardization.

Keywords:

Data Transformation Data Warehousing Electronic Health Records Medical Informatics

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Area of Science:

Biomedical Informatics
Data Science
Clinical Research Informatics

Background:

Standardizing heterogeneous clinical data is crucial for large-scale research.
The OMOP Common Data Model (CDM) facilitates data standardization.
Current ETL processes for OMOP CDM are often manual and complex.

Purpose of the Study:

To develop an automated, mapping-driven ETL pipeline for converting CSV clinical datasets into OMOP CDM v5.4.
To improve the efficiency, reproducibility, and maintainability of ETL processes for OMOP CDM.

Main Methods:

Developed a Python-based ETL pipeline utilizing metadata processing and dbt-generated SQL models.
Implemented a layered architecture (raw, staging, intermediate, OMOP) in PostgreSQL.
Incorporated Rabbit-in-a-Hat-derived mappings and robust CSV handling.
Automated the generation of transformation logic, requiring only manual mapping definitions.

Main Results:

The pipeline successfully converts CSV data to OMOP CDM v5.4.
Automated generation of downstream models enhances efficiency and reusability.
The system improves reproducibility, transparency, and maintainability of ETL processes.

Conclusions:

The automated ETL pipeline significantly simplifies and accelerates the conversion of clinical data to OMOP CDM.
This approach enables efficient reuse of data transformation logic across various research settings.
Manual mapping definition is the primary manual step, streamlining the overall ETL workflow.