PhytoMine

PhytoMine provides integrated access to genomic and annotation data from Phytozome (the Plant Comparative Genomics portal managed by the Department of Energy's Joint Genome Institute) using the InterMine data warehouse to support comparative genomics across Viridiplantae.

Key Features:

• Comprehensive Data Integration: Integrates genomic and annotation data from 81 assembled and annotated genomes across 78 species within Viridiplantae using InterMine's extensible data model.
• Customizable Query Facility: Offers a customizable query builder and genomic region search capability for precise extraction of genomic information.
• Statistical Analysis Tools: Provides widgets for statistical analyses to assist interpretation of complex plant genomic data.
• Data Export Options: Exports query results in multiple commonly used formats for compatibility with other bioinformatics tools.
• Extensibility and Customization: Built on a fully extensible framework that permits addition of new functionalities and tools.
• Web Services and Programming Support: Exposes web services with client libraries in five programming languages to enable integration into computational workflows.

Scientific Applications:

• Comparative Genomics: Enables investigation of evolutionary relationships and orthology across plant species represented in Phytozome.
• Gene Function and Annotation Studies: Supports gene-centric analyses and functional annotation comparisons across genomes.
• Genomic Diversity and Applied Research: Facilitates analysis of genomic diversity across Viridiplantae for basic research and applied biotechnology studies.

Methodology:

Implements the InterMine data warehouse framework to model, integrate, and manage large-scale genomic datasets sourced from Phytozome.