SoyMine

SoyMine integrates and manages soybean genomic and genetic data to support integrative analyses in legume genomics.

Key Features:

• Data Integration: Integrates genomic data from the Legume Information Systems (LIS) multi-species chado database and genetic data from Soybase into a unified repository.
• Customizable Query Facility: Provides a fast, customizable query facility for retrieving specific data subsets.
• Extensible Data Model: Supports integration of new data types through an extensible data model.
• Analysis Tools: Includes a flexible query builder, genomic region search, and a library of widgets for statistical analyses.
• Data Export Options: Exports query and analysis results in multiple commonly used formats.
• Extensibility and Web Services: Delivers an extensible framework with web services and client libraries available in five widely-used programming languages.

Scientific Applications:

• Genetic Mapping: Supports retrieval and integration of genetic markers and mapping data for soybean genetics studies.
• Comparative Genomics: Enables cross-species data comparison within legume genomics using multi-species datasets.
• Functional Annotation: Facilitates functional annotation by combining genomic and genetic evidence for soybean genes.
• Crop Trait Research: Assists research aimed at improving crop yield, disease resistance, and nutritional quality through integrated data analyses.

Methodology:

Built on the InterMine open-source data warehouse framework, integrating the LIS multi-species chado database and Soybase, and exposing functionality via web services with client libraries in five programming languages.