Synthetic biology open language visual (SBOL visual) version 3.0

Area of Science:

• Synthetic Biology
• Bioinformatics
• Molecular Engineering

Background:

• Diagrams are crucial for communicating genetic designs and functional relationships in synthetic biology.
• Emerging conventions for these diagrams require systematization for a coherent visual language.
• The Synthetic Biology Open Language Visual (SBOL Visual) standard aims to organize these conventions.

Purpose of the Study:

• To detail version 3.0 of the SBOL Visual standard, a significant revision.
• To establish a coherent visual language for expressing the structure and function of genetic designs.
• To update the standard based on the SBOL 3 data model.

Main Methods:

• Defining diagrams and glyphs with respect to the SBOL 3 data model.
• Removing deprecated elements from the glyph collection, including specific glyphs and BioPAX alternatives.
• Adapting representation of subsystem mappings to align with SBOL 3 constraints.

Main Results:

• SBOL Visual 3.0 is now defined relative to the SBOL 3 data model, differing from SBOL Visual 2.
• The use of dashed undirected lines for subsystem mappings has been removed pending further SBOL 3 constraint representation.
• Deprecated glyphs and BioPAX alternatives have been removed, streamlining the standard.

Conclusions:

• SBOL Visual 3.0 provides a modernized and systematized approach to visualizing genetic designs.
• The alignment with the SBOL 3 data model ensures consistency and future compatibility.
• This revision facilitates clearer communication and standardization in synthetic biology engineering.