MaizeMine

MaizeMine provides an integrated data warehouse for MaizeGDB that aggregates heterogeneous maize genetics and genomics datasets to support querying and analysis.

Key Features:

• Data Integration and Customization: Leverages the extensible InterMine data model to incorporate and integrate new and heterogeneous maize data types and large biological datasets.
• MaizeGDB Integration: Integrates data specifically from the Maize Genetics and Genomics Database (MaizeGDB) within the warehouse.
• Query Facility: Provides a flexible query builder for fast, customizable retrieval of genomic information.
• Genomic Region Search: Includes tools to search and retrieve data for specific genomic regions of the maize genome.
• Statistical Analysis Widgets: Offers a library of widgets for performing statistical analyses on retrieved datasets.
• Data Export Options: Supports export of query results in multiple commonly used formats for downstream analysis.
• Extensibility and Web Services: Implements an extensible framework with web services and client libraries in five programming languages to enable programmatic access and addition of tools.

Scientific Applications:

• Gene Discovery: Aggregates genomic and annotation data to support identification and characterization of maize genes.
• Functional Genomics: Facilitates functional genomics studies through integrated annotations and analytical widgets.
• Genetic Variation and Trait Association: Enables investigation of genetic variation and trait associations by combining diverse datasets and query/analysis tools.
• Data Synthesis for Maize Research: Allows synthesis of heterogeneous datasets to support comprehensive maize genetics and genomics investigations.

Methodology:

Built on the open-source InterMine framework and its extensible data model to integrate heterogeneous maize genetics and genomics datasets, exposing web services with client libraries in five programming languages and an architecture that supports addition of new data types and analytical tools.