CMToolkit is a python-based application designed to migrate and harmonize clinical cohorts from CSV format into the OHDSI OMOP CDM schema. This procedure increases the interoperability of the data by allowing the exportation of several cohorts into a new system reusing the same scripts.

• The CMToolkit proposes a strategy for semi-automatic harmonisation of large amounts of medical concepts in clinical studies.


• It creates new opportunities for the study of rare conditions, where typically isolated cohorts do not provide enough statistical evidence.


• The results can augment clinical knowledge by automatically computing new patient information during the migration stage.