Abstract
People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.3 of SBOL Visual, which builds on the prior SBOL Visual 2.2 in several ways. First, the specification now includes higher-level “interactions with interactions,” such as an inducer molecule stimulating a repression interaction. Second, binding with a nucleic acid backbone can be shown by overlapping glyphs, as with other molecular complexes. Finally, a new “unspecified interaction” glyph is added for visualizing interactions whose nature is unknown, the “insulator” glyph is deprecated in favor of a new “inert DNA spacer” glyph, and the polypeptide region glyph is recommended for showing 2A sequences.
Highlights
This document does not contain technology or technical data controlled under either the U.S International Traffic in Arms Regulations or the U.S Export Administration Regulations
Baig et al.: Synthetic biology open language visual developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs
A number of requirements are placed on all SBOL Visual glyphs in order to ensure both the clarity of diagrams and 2 the ease with which they can be constructed: 1. A glyph SHOULD have its meaning defined by associating the glyph with at least one ontology definition. 4
Summary
People who engineer biological organisms often find it useful to draw diagrams in order to communicate both the 2 structure of the nucleic acid sequences that they are engineering and the functional relationships between sequence 3 features and other molecular species. Some typical practices and conventions have begun to emerge for such 4 diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language 5 for expressing the structure and function of genetic designs. We aim to make this language simple 6 and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, 7 and styled—in particular, it should be readily possible to create diagrams either by hand or using a wide variety of 8 software programs. Means are provided for extending the language with new and custom diagram elements, 9 and for adoption of useful new elements into the language
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