Synthetic biology open language visual (SBOL visual) version 2.2

Hasan Baig; Pedro Fontanarrosa; Vishwesh Kulkarni; James McLaughlin; Prashant Vaidyanathan; Bryan Bartley; Swapnil Bhatia; Shyam Bhakta; Michael Bissell; Kevin Clancy; Robert Sidney Cox; Angel Goñi Moreno; Thomas Gorochowski; Raik Grunberg; Augustin Luna; Curtis Madsen; Goksel Misirli; Tramy Nguyen; Nicolas Le Novere; Zachary Palchick; Matthew Pocock; Nicholas Roehner; Herbert Sauro; James Scott-Brown; John T. Sexton; Guy-Bart Stan; Jeffrey J. Tabor; Marta Vazquez Vilar; Christopher A. Voigt; Anil Wipat; David Zong; Zach Zundel; Jacob Beal; Chris Myers

doi:10.1515/jib-2020-0014

Open Access Published by De Gruyter June 10, 2020

Synthetic biology open language visual (SBOL visual) version 2.2

Hasan Baig , Pedro Fontanarrosa , Vishwesh Kulkarni , James McLaughlin , Prashant Vaidyanathan , Bryan Bartley , Swapnil Bhatia , Shyam Bhakta , Michael Bissell , Kevin Clancy , Robert Sidney Cox , Angel Goñi Moreno , Thomas Gorochowski , Raik Grunberg , Augustin Luna , Curtis Madsen , Goksel Misirli , Tramy Nguyen , Nicolas Le Novere , Zachary Palchick , Matthew Pocock , Nicholas Roehner , Herbert Sauro , James Scott-Brown , John T. Sexton , Guy-Bart Stan , Jeffrey J. Tabor , Marta Vazquez Vilar , Christopher A. Voigt , Anil Wipat , David Zong , Zach Zundel , Jacob Beal and Chris Myers

From the journal Journal of Integrative Bioinformatics

https://doi.org/10.1515/jib-2020-0014

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 2.2 of SBOL Visual, which builds on the prior SBOL Visual 2.1 in several ways. First, the grounding of molecular species glyphs is changed from BioPAX to SBO, aligning with the use of SBO terms for interaction glyphs. Second, new glyphs are added for proteins, introns, and polypeptide regions (e. g., protein domains), the prior recommended macromolecule glyph is deprecated in favor of its alternative, and small polygons are introduced as alternative glyphs for simple chemicals.

Keywords: diagrams; SBOL visual; standards

Corresponding author: Chris Myers, University of Utah, Salt Lake City, USA, E-mail: editors@sbolstandard.org

Received: 2020-03-30

Accepted: 2020-04-16

Published Online: 2020-06-10

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

Synthetic biology open language visual (SBOL visual) version 2.2

Abstract

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