Translation of SBGN maps: Process Description to Activity Flow

Area of Science:

• Systems Biology
• Bioinformatics
• Computational Biology

Background:

• The Systems Biology Graphical Notation (SBGN) offers standardized graphical languages for biological networks.
• SBGN includes Process Descriptions (PD), Entity Relationships (ER), and Activity Flows (AF).
• SBGN PD maps are often complex, necessitating simplified representations.

Purpose of the Study:

• To develop methods for simplifying complex SBGN Process Descriptions (PD) maps.
• To translate SBGN PD maps into the more abstract SBGN Activity Flows (AF) format.

Main Methods:

• Defined template-based translations from SBGN PD to SBGN AF maps.
• Explored map layout and interactive navigation between PD and AF maps.
• Implemented translation methods within the SBGN-ED software.

Main Results:

• SBGN PD maps are significantly reduced in size and complexity when translated to SBGN AF.
• Template-based translation allows users to focus on specific biological system aspects.
• Interactive navigation facilitates exploration between PD and AF map representations.

Conclusions:

• Translation of SBGN PD to AF creates smaller, more manageable biological network visualizations.
• This work is a foundational step for inter-language translation within SBGN.
• Future research can explore translation methods between other SBGN languages.