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Synthetic biology open language visual (SBOL visual) version 2.2

Lookup NU author(s): James Alastair McLaughlin McLaughlin, Dr Goksel Misirli, Dr Matthew Pocock, Professor Anil Wipat, Professor Christopher Myers

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

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.

Publication metadata

Author(s): Baig H, Fontanarrosa P, Kulkarni V, McLaughlin J, Vaidyanathan P, Bartley B, Bhatia S, Bhakta S, Bissell M, Clancy K, Cox RS, Moreno AG, Gorochowski T, Grunberg R, Luna A, Madsen C, Misirli G, Nguyen T, Le Novere N, Palchick Z, Pocock M, Roehner N, Sauro H, Scott-Brown J, Sexton JT, Stan G-B, Tabor JJ, Vilar MV, Voigt CA, Wipat A, Zong D, Zundel Z, Beal J, Myers C

Publication type: Article

Publication status: Published

Journal: Journal of Integrative Bioinformatics

Year: 2020

Volume: 17

Issue: 2-3

Online publication date: 10/06/2020

Acceptance date: 16/04/2020

Date deposited: 01/11/2023

ISSN (electronic): 1613-4516

Publisher: de Gruyter

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

DOI: 10.1515/jib-2020-0014

PubMed id: 32543457

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