Journal of Integrative Bioinformatics
Baig, H., Fontanarrosa, P., Kulkarni, V., McLaughlin, J.,
Vaidyanathan, P., Bartley, B., Bhatia, S., Bhakta, S., Bissell, M.,
Clancy, K., Cox, R. S., Go?i Moreno, A., Gorochowski, T. E.,
Grunberg, R., Luna, A., Madsen, C., Misirli, G., Nguyen, T., Le
Novere, N., ... Myers, C. (2020). Synthetic biology open language
visual (SBOL visual) version 2.2. Journal of Integrative Bioinformatics.
Advance online publication.
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10.1515/jib-2020-0014
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Journal of Integrative Bioinformatics 2020; 20200014
Hasan Baig, Pedro Fontanarrosa, Vishwesh Kulkarni, James McLaughlin,
Prashant Vaidyanathan, Bryan Bartley, Swapnil Bhatia, Shyam Bhakta,
Michael Bissell, Kevin Clancy, Robert Sidney Cox, Angel Go?i 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*
Synthetic biology open language visual
(SBOL visual) version 2.2
Received March 30, 2020; accepted April 16, 2020
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
*Corresponding author: Chris Myers, University of Utah, Salt Lake City, USA, E-mail: editors@
Hasan Baig: University of Connecticut, Storrs, USA
Pedro Fontanarrosa and Zach Zundel: University of Utah, Salt Lake City, USA.
(P. Fontanarrosa)
Vishwesh Kulkarni: University of Warwick, Coventry, UK
James McLaughlin, Angel Go?i Moreno and Anil Wipat: Newcastle University, Newcastle upon Tyne, UK
Prashant Vaidyanathan: Microsoft Research, Cambridge, UK
Bryan Bartley, Tramy Nguyen, Nicholas Roehner and Jacob Beal: Raytheon BBN Technologies, Cambridge, USA.
0000-0002-1663-5102 (J. Beal)
Swapnil Bhatia and Curtis Madsen: Boston University, Boston, USA
Shyam Bhakta, John T. Sexton, Jeffrey J. Tabor and David Zong: Rice University, Houston, USA. (D. Zong)
Michael Bissell: Shipyard Toolchains LLC, Emeryville, USA
Kevin Clancy: Thermo Fisher Scientific, San Diego, USA
Robert Sidney Cox: Kobe University, Kobe, Japan
Thomas Gorochowski: University of Bristol, Bristol, UK
Raik Grunberg: KAUST, Thuwal, Saudi Arabia.
Augustin Luna: Harvard Medical School, Boston, USA
Goksel Misirli: Keele University, Keele, UK
Nicolas Le Novere: Babraham Institute, Cambridge, UK
Zachary Palchick: Zymergen, Emeryville, USA
Matthew Pocock: Turing Ate My Hamster, Ltd., Newcastle, UK
Herbert Sauro: University of Washington, Seattle, USA
James Scott-Brown: University of Oxford, Oxford, UK
Guy-Bart Stan: Imperial College, London, UK
Marta Vazquez Vilar: Universitat Politecnica de Valencia, Valencia, Spain
Christopher A. Voigt: MIT, Cambridge, USA
Open Access. ? 2020 Hasan Baig et al., published by De Gruyter.
4.0 Public License.
This work is licensed under the Creative Commons Attribution
2
H. Baig et al.: SBOL Visual 2.2
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.
Hasan Baig
Pedro Fontanarrosa
Vishwesh Kulkarni
James McLaughlin
Prasant Vaidyanathan
Editors:
University of Connecticut, USA
University of Utah, USA
University of Warwick, UK
Newcastle University, UK
Microsoft Research, UK
sbol-editors@
Chair:
Chris Myers
University of Utah, USA
Additional authors, by last name:
Bryan Bartley
Jacob Beal
Swapnil Bhatia
Shyam Bhakta
Michael Bissell
Kevin Clancy
Robert Sidney Cox
Angel Goni 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
Chris Voigt
Anil Wipat
David Zong
Zach Zundel
Raytheon BBN Technologies, USA
Raytheon BBN Technologies, USA
Boston University, USA
Rice University, USA
Shipyard Toolchains LLC, USA
Thermo Fisher Scientific, USA
Kobe University, Japan
Newcastle University, UK
University of Bristol, UK
KAUST, Saudi Arabia
Harvard Medical School, USA
Sandia National Laboratories, USA
Keele University, UK
University of Utah, USA
Babraham Institute, UK
Zymergen, USA
Turing Ate My Hamster, Ltd., UK
Raytheon BBN Technologies, USA
University of Washington, USA
University of Oxford, UK
Rice University, USA
Imperial College, UK
Rice University, USA
Universitat Politecnica de Valencia, Spain
MIT, USA
Newcastle University, UK
Rice University, USA
University of Utah, USA
Version 2.2
March, 2020
Copyright (C) all authors listed on the front page of this document.
This work is made available under the Creative Commons Attribution 4.0 International Public License.
Copyright XXXX The Author(s). Published by Journal of Integrative Bioinformatics.
This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License ().
Synthetic Biology Open
Language Visual (SBOL Visual) Version 2.2
1 Purpose
1.1 Relation to Data Models . . . . . . . . . .
2 Relation to other Standards
3 SBOL Specification Vocabulary
3.1 Term Conventions . . . . . . . . . . . . .
3.2 SBOL Class Names . . . . . . . . . . . .
4 SBOL Glyphs
4.1 Requirements for Glyphs . . . . . . . . . .
4.2 Reserved Visual Properties . . . . . . . .
4.3 Extending the Set of Glyphs . . . . . . . .
5 SBOL Visual Diagram Language
5.1 Nucleic Acid Backbone . . . . . . . . . . .
5.2 Nucleic Acid Sequence Features . . . . .
5.3 Molecular Species . . . . . . . . . . . . .
5.4 Interaction . . . . . . . . . . . . . . . . . .
5.5 Modules . . . . . . . . . . . . . . . . . . .
5.6 Labels . . . . . . . . . . . . . . . . . . . .
5.7 Annotations . . . . . . . . . . . . . . . . .
5.8 Criteria for Compliance with SBOL Visual
A SBOL Visual Glyphs
A.1 Sequence Feature Glyphs . . . . . . . . .
A.2 Molecular Species Glyphs . . . . . . . . .
A.3 Interaction Glyphs . . . . . . . . . . . . .
A.4 Interaction Node Glyphs . . . . . . . . . .
B Examples
C Relationship to SBOL Visual 1.0
References
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Copyright XXXX The Author(s). Published by Journal of Integrative Bioinformatics.
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