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BY 4.0 license Open Access Published by De Gruyter October 20, 2021

Synthetic biology open language visual (SBOL visual) version 3.0

Hasan Baig , Pedro Fontanarossa ORCID logo , James McLaughlin , James Scott-Brown , Prashant Vaidyanathan , Thomas Gorochowski , Goksel Misirli , Jacob Beal ORCID logo EMAIL logo and Chris Myers

Abstract

People who engineer biological organisms often find it useful to draw diagrams in order to communicate both the structure of the nucleic acid sequences that they are engineering and the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 3.0 of SBOL Visual, a new major revision of the standard. The major difference between SBOL Visual 3 and SBOL Visual 2 is that diagrams and glyphs are defined with respect to the SBOL 3 data model rather than the SBOL 2 data model. A byproduct of this change is that the use of dashed undirected lines for subsystem mappings has been removed, pending future determination on how to represent general SBOL 3 constraints; in the interim, this annotation can still be used as an annotation. Finally, deprecated material has been removed from collection of glyphs: the deprecated “insulator” glyph and “macromolecule” alternative glyphs have been removed, as have the deprecated BioPAX alternatives to SBO terms.


Corresponding author: Jacob Beal, Raytheon BBN Technologies, Cambridge, USA, E-mail:

Award Identifier / Grant number: 1522074

  1. Author contribution: All authors have accepted responsibility for the entire content of this manuscript and approved its submission.

  2. Research funding: The results of this work was funded by grant National Science Foundation.

  3. Conflict of interest statement: Authors state no conflict of interest.

Received: 2021-05-12
Accepted: 2021-08-26
Published Online: 2021-10-20

© 2021 Hasan Baig et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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