BDI-Kit: An AI-powered toolkit for biomedical data harmonization

The wide availability of biomedical data, coupled with advanced analytics, holds unprecedented promise for scientific discovery and improved patient care; yet, heterogeneity across datasets remains a major barrier. Given the inherent diversity of biomedical domains, one-size-fits-all solutions are impractical. Despite decades of active research and numerous methods for automating data integration, there is a scarcity of open-source tools capable of handling this complexity. To address these challenges, we introduce Biomedical Data Integration and Harmonization Toolkit (BDI-Kit), an extensible toolkit designed for human-AI collaboration that provides a diverse suite of harmonization methods. It offers two complementary interfaces: a Python API that supports the creation of computational pipelines for harmonization and an AI-assisted chat interface that enables domain experts to perform harmonization using natural language. In this paper, we describe BDI-Kit and demonstrate its capabilities through real-world use cases. By simplifying data harmonization, BDI-Kit empowers researchers and practitioners, facilitating effective exploration and accelerating scientific discovery and clinical research.