MouseDEF

MouseDEF is a modular, open-source framework for managing, annotating, and analyzing data generated in mouse-based biomedical research. It provides a standardized data model that unifies behavioral, genetic, imaging, electrophysiological, and molecular measurements across experiments, enabling cross-study comparisons and data reuse. The project emphasizes reproducibility, interoperability, and scalability, and is designed to integrate with existing data standards and analysis pipelines.

Architecture and features: The framework consists of a core data model, a set of domain-specific modules, and a plugin system that allows researchers to add custom analyses. It supports common data formats, metadata schemas, and ontologies; it includes versioned datasets, provenance tracking, and reproducible workflows via notebooks or pipelines. It also offers APIs for programmatic access and integration with computing clusters and high-performance storage.

Development and use: MouseDEF originated from a collaboration among neuroscience labs and data science groups to address fragmentation in mouse research data. Since its inception, it has been adopted by university and industry labs to standardize phenotyping studies, longitudinal imaging cohorts, and multi-modal experiments. The project maintains an active public repository and community governance to guide feature requests and compatibility across versions.

Impact and reception: Advocates cite improved data sharing, reproducibility, and efficiency in multicenter studies. Critics note a learning curve and the need for consistent data collection practices to fully realize benefits.

See also: XNAT, Neurodata Without Borders (NWB), Brain Imaging Data Structure (BIDS).