YeastMine

YeastMine provides integrated access to heterogeneous Saccharomyces cerevisiae datasets using the InterMine data warehouse framework for flexible querying and computational analysis.

Key Features:

• Data Integration and Extensibility: Implements InterMine's flexible data model to integrate heterogeneous biological data and enable schema extensions.
• Customizable Query Facility: Offers a flexible query builder for constructing tailored queries against integrated yeast datasets.
• Genomic Region Search: Supports genomic region searches to retrieve features and annotations within specified segments of the Saccharomyces cerevisiae genome.
• Statistical Analysis Tools: Provides a library of "widgets" for performing statistical analyses on query results.
• Data Export Options: Allows export of query results in commonly used bioinformatics file formats for downstream analysis.
• Web Services and Programming Language Support: Exposes web services with client libraries available in five programming languages for programmatic access.

Scientific Applications:

• Genomic Studies: Integrates genome annotations and feature data to support analyses of gene structure and genomic loci in Saccharomyces cerevisiae.
• Gene Expression Analysis: Combines expression datasets with annotations to facilitate analysis of transcriptional patterns.
• Protein Interaction Studies: Links protein interaction data to gene and protein annotations for network and interaction analyses.
• Metabolic Pathway Investigations: Aggregates pathway and metabolic information to support analysis of metabolic networks and pathway components.
• Hypothesis Generation and Experimental Design: Enables cross-dataset queries to generate hypotheses and inform experimental design and model validation.

Methodology:

Built on the InterMine data warehouse framework for integration, storage, and efficient retrieval of biological datasets, with support for schema extensions and web-service access.