MedicMine

MedicMine integrates heterogeneous biological datasets for Medicago truncatula to enable genomic region searches, gene-list analyses, and statistical analyses using the InterMine data warehouse platform.

Key Features:

• Data Integration: Leverages the InterMine open-source data warehouse with an extensible data model to combine heterogeneous Medicago truncatula datasets into a unified database.
• Flexible Query Facility: Provides a configurable query builder to perform customized searches across integrated datasets.
• Genomic Region Search: Supports targeted searches and analyses of specific genomic segments.
• Statistical Analysis Tools: Offers a library of 'widgets' for conducting statistical analyses on integrated data.
• Export Options: Allows export of query and analysis results in multiple commonly used file formats for downstream analysis.
• Extensibility and Customization: Implements a fully extensible framework that enables addition of new tools and functionalities.
• Web Services and Programming Support: Exposes web services with client libraries available in five programming languages for integration with external software.

Scientific Applications:

• Gene-list analysis: Identifies and annotates gene sets from Medicago truncatula for downstream interpretation.
• Genomic region analysis: Investigates features and annotations within selected genomic intervals.
• Statistical analysis of integrated datasets: Performs statistical assessments on combined genomic, gene, and annotation data.
• Plant biology and genetics research: Supports research in Medicago truncatula genomics, plant biology, and genetics through integrated data and analysis tools.

Methodology:

Implements the InterMine data warehouse framework with an extensible data model, a configurable query builder, genomic region search functionality, statistical 'widgets', and web services with client libraries in five programming languages.