IndigoMine

IndigoMine integrates and enables exploration of annotations in newly sequenced microbial genomes to support genomic data integration and analysis.

Key Features:

• Data Integration: IndigoMine uses the open-source InterMine system to construct data warehouses that integrate diverse and heterogeneous biological data sources.
• Customizable Query Facility: Provides a flexible query builder enabling tailored searches across integrated datasets.
• Extensible Data Model: Employs an extensible data model that allows incorporation of new data types as scientific knowledge expands.
• Analysis Tools: Includes genomic region search capabilities and a library of 'widgets' that perform various statistical analyses on genomic data.
• Export Options: Allows export of query and analysis results in multiple commonly used formats compatible with other bioinformatics tools.
• Extensibility for Developers: Offers a framework that permits developers to add new functionalities and tools.
• Web Services and Client Libraries: Exposes a comprehensive set of web services with client libraries available in five programming languages for programmatic access.

Scientific Applications:

• Microbial Genome Annotation: Aids exploration and annotation of newly sequenced microbial genomes.
• Genomic Research and Biotechnology: Supports both basic genomic studies and applied biotechnology research.
• Complex Data Integration for Microbial Genetics: Enables integration of heterogeneous datasets to facilitate studies of microbial genetics and their applications.

Methodology:

Implements data warehousing and integration using the open-source InterMine framework and exposes data via web services with client libraries.