Carrot-CDM

Welcome to our repo for python tools used by/with the Carrot project. The primary functionality is used for performing ETL on health datasets, converting them to the OHDSI Common Data Model (CDM), via a command line interface.

CaRROT-CDM contains a pythonic version¹ of the OHDSI CDM, implemented via the class CommonDataModel. CDM tables, such as "Person" are defined as classes (e.g. Person) within the code base.

The primary purpose of the CaRROT-CDM package is to Extract input datasets and Transform them using mapping rules defined in a json file, outputting formatted datasets in tsv format that can be Loaded into a database or other destination (ETL).

Getting Started

To get started with the ETL process, follow the instructions for installing the CaRROT-CDM package and running the ETL on the following pages:

ETL

1. Frequently Asked Questions
2. Installing
3. About the ETL Process
4. Guide
   1. Configuration
   2. Extract
   3. Transform
   4. Load

Guides

More detailed guides and documentation for users and developers can be found in the following locations:

User Guide Developer Guide

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1. In the default setup a slightly (visit_detail_id link has been removed from Measurement, Observation and Condition Occurrence tables) modified CDM version 5.3.1 is used to define a subset of tables in python. ↩