OakMine

OakMine integrates heterogeneous biological datasets using the InterMine framework to provide programmable querying and analysis of large-scale genomic and biological data.

Key Features:

• Data Integration: Aggregates diverse biological datasets into a unified InterMine-backed database.
• Extensible Data Model: Exposes a fully extensible data model to incorporate new data types.
• Customizable Query Facility: Provides a flexible query builder supporting intricate searches, including genomic region searches.
• Analysis Tools: Includes a library of widgets for statistical analyses and detailed data examination.
• Export Options: Exports results in multiple commonly used formats for downstream analysis.
• Web Services and Client Libraries: Exposes web services with client libraries available in five programming languages.
• Developer Extensibility: Employs an extensible architecture that enables developers to add new tools and features.

Scientific Applications:

• Genomics: Supports genomic region searches and integration of large-scale genomics datasets for query-driven analyses.
• Large-scale Biological Database Construction: Enables building integrated databases from heterogeneous biological sources.
• Integrative Analyses: Facilitates cross-dataset statistical analyses using the included analysis widgets.

Methodology:

Built on the open-source InterMine framework; uses an extensible architecture and data model; provides a customizable query builder including genomic region searches; includes a library of analysis widgets; exposes web services and client libraries in five programming languages; and supports export to multiple common formats.