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Synthetic biology open language visual (SBOL visual) version 2.2

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

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Authors

Hasan Baig

Pedro Fontanarrosa

Vishwesh Kulkarni

James McLaughlin

Prashant Vaidyanathan

Bryan Bartley

Swapnil Bhatia

Shyam Bhakta

Michael Bissell

Kevin Clancy

Robert Sidney Cox

Angel Goni Moreno

Thomas Gorochowski

Raik Grunberg

Augustin Luna

Curtis Madsen

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



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.

Journal Article Type Article
Acceptance Date Apr 16, 2020
Online Publication Date Jun 10, 2020
Publication Date Jun 10, 2020
Publicly Available Date May 26, 2023
Journal Journal of integrative bioinformatics
Print ISSN 1613-4516
Publisher De Gruyter
Peer Reviewed Peer Reviewed
Volume 17
Issue 2-3
Article Number 20200014
DOI https://doi.org/10.1515/jib-2020-0014
Keywords Diagrams, SBOL visual, Standards
Publisher URL https://doi.org/10.1515/jib-2020-0014

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