Tripal MapViewer

Tripal MapViewer visualizes and compares genetic maps to enable analysis of molecular markers, quantitative trait loci (QTLs), and linkage relationships within Tripal and Chado-based genomic databases.

Key Features:

• Interactive map visualization: Renders entire genetic maps and specific linkage groups with representations of molecular markers, quantitative trait loci (QTLs), and heritable phenotypic markers.
• Graphical comparison: Generates dot plots and correspondence matrices for maps that share common markers to analyze similarities and differences between genetic maps.
• Tripal API integration: Integrates map data with the Tripal API to connect map records to Tripal site content and search functions.
• Chado and Drupal integration: Stores and retrieves map and feature data using the Chado schema and operates within Drupal-based Tripal sites.
• Materialized views and custom queries: Supports custom database queries and creation of materialized views to optimize data storage and performance within Chado.
• D3.js implementation: Implements visualizations using D3.js for dynamic, browser-based rendering of map graphics.

Scientific Applications:

• Plant genomics and breeding: Supports comparative mapping and breeding research by enabling visualization and comparison of genetic maps.
• Genome Database for Rosaceae: Deployed for genetic map visualization and comparative analysis.
• CottonGen: Used for visualization and comparison of cotton genetic maps.
• Citrus Genome Database: Employed to display and compare citrus genetic maps.
• Vaccinium Genome Database: Utilized for map visualization and comparative mapping in Vaccinium research.
• Cool Season Food Legume Database: Applied to visualize and compare legume genetic maps.
• Hardwood Genomics Web and TreeGenes (development): Under development for use with Hardwood Genomics Web and TreeGenes for forest tree genomic mapping.

Methodology:

renders genetic maps and linkage groups with markers, QTLs, and heritable phenotypic markers; generates dot plots and correspondence matrices; stores and accesses data via the Chado schema within Drupal and Tripal; supports custom SQL queries and materialized views for data optimization; and implements interactive browser-based visualizations using D3.js.