Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

Area of Science:

• Bioinformatics
• Computational Biology
• Systems Biology

Background:

• Biological pathway visualization is crucial for understanding complex cellular processes.
• Existing tools may lack flexibility or advanced data integration capabilities.

Purpose of the Study:

• To introduce Escher, a web application for effective biological pathway visualization.
• To highlight Escher's unique features for designing, visualizing, and sharing pathway maps.

Main Methods:

• Development of a web application utilizing Scalable Vector Graphics (SVG) and Data-Driven Documents (D3).
• Implementation of semi-automated pathway map generation using user data and genome-scale models.
• Integration of multi-omics data types (genomics, proteomics, metabolomics, fluxomics) with pathway reactions.

Main Results:

• Escher enables rapid design of new pathway maps with automated suggestions.
• Users can visualize diverse genomic and metabolomic data on biological pathways.
• The application leverages web technologies for easy adaptation, extension, sharing, and embedding of visualizations.

Conclusions:

• Escher provides a powerful and flexible platform for biological pathway visualization.
• Its features facilitate the integration and interpretation of multi-omics data.
• The Escher development approach can inform future visualization tool development.