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2026-06-23

OMOP Mapping Tools

Mapping source data to OMOP can be challenging and requires specialist skills and tools. This page describes the tools available and the support HDR UK can offer.

Separate mapping from ETL

It is easier to separate the mapping logic from the ETL step. This allows non-technical subject matter experts to create mapping rules (using Carrot Mapper) that are then applied by an automated ETL tool (Carrot-CDM).

Supported tools

Developed by: OHDSI

White Rabbit is typically the first tool used in the ETL process. It scans your source data and produces a detailed report on tables, fields, and values.

What it does:

  • Scans source databases (MS Access, CSV, SQL databases, etc.)
  • Produces a Scan Report describing table names, field names, data types, and value frequencies
  • Outputs a structured file used as input to Carrot Mapper

Output: A ScanReport file (Excel format)

Running White Rabbit
# White Rabbit is a Java application — download from OHDSI GitHub
java -jar WhiteRabbit.jar

White Rabbit on OHDSI

Developed by: HDR UK / CO-CONNECT project

Carrot Mapper is a web-tool that maps the White Rabbit output to generate a JSON mapping file that defines the ETL guidelines for your dataset.

What it does:

  • Accepts the White Rabbit ScanReport as input
  • Provides a web interface for mapping source fields to OMOP CDM fields
  • Generates a JSON Mapping File used by Carrot-CDM

Output: A JSON mapping file

Carrot Mapper documentation

Developed by: HDR UK / CO-CONNECT project

Carrot-CDM automates the extraction of pseudonymised data, transformation to OMOP CDM, and loading into the query tool database.

What it does:

  • Takes your source data and the Carrot Mapper JSON mapping file as inputs
  • Automates the full ETL process to produce an OMOP-formatted database
  • Loads data into a format ready for Bunny or similar query tools
Running Carrot-CDM
pip install carrot-cdm
carrot run --rules mapping_rules.json --input source_data/

Carrot-CDM documentation

Process overview

flowchart LR
    SD[(Source Data)] --> WR[White Rabbit\nData Profiling]
    WR -->|ScanReport| CM[Carrot Mapper\nOMOP Mapping]
    CM -->|JSON Mapping File| CCDM[Carrot-CDM\nETL]
    SD --> CCDM
    CCDM --> OMOP[(OMOP Database)]

Alternative tools

CaRROT tools are not mandatory

HDR UK has worked with and can support the CaRROT toolchain. Other tools are available:

Alternative Purpose Notes
Usagi Manual OMOP code mapping Developed by OHDSI; useful for term-level mapping
Commercial ETL vendors End-to-end OMOP ETL Various vendors available

HDR UK mapping support

HDR UK and partners at the Health Informatics Centre (HIC), University of Dundee offer OMOP mapping services using CaRROT tools.

Need mapping support?

Contact your HDR UK contact or email gateway@hdruk.ac.uk to discuss OMOP mapping support options.