ModMine

ModMine aggregates heterogeneous genomic and functional genomics datasets and provides integrated querying and analysis support for large-scale projects such as modENCODE.

Key Features:

• Complex Data Integration: Integrates diverse datasets from multiple sources into cohesive biological databases for comprehensive coverage.
• Customizable Query Facility: Provides a flexible query builder that enables fast, precise retrieval of integrated data tailored to specific research questions.
• Extensible Data Model: Supports addition of new data types and schema extensions to accommodate evolving scientific data.
• Analysis Tools: Includes genomic region search capabilities and a library of "widgets" for statistical and exploratory analyses.
• Data Export Options: Exports query and analysis results in numerous commonly used formats to support downstream workflows.
• Web Services and Client Libraries: Exposes comprehensive web services and client libraries available in five widely used programming languages for programmatic access.

Scientific Applications:

• Large-scale functional genomics projects (e.g., modENCODE): Organizes, retrieves, and integrates heterogeneous datasets to support project-scale data management and analysis.
• Gene function and regulation analysis: Enables investigation of gene function, regulatory elements, and regulatory relationships within integrated datasets.
• Interaction network and comparative analyses: Supports analysis of interaction networks and comparative studies across various organisms.

Methodology:

Built using the InterMine open-source framework to construct extensible data warehouses that integrate heterogeneous biological datasets and expose web services and client libraries.