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 ORCID: https://orcid.org/0000-0002-2454-7188, 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 and Myers, C (2020) Synthetic biology open language visual (SBOL visual) version 2.2. Journal of integrative bioinformatics.

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[16134516 - Journal of Integrative Bioinformatics] Synthetic biology open language visual (SBOL visual) version 2.2.pdf - Published Version

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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.

Item Type: Article
Additional Information: The Journal of Integrative Bioinformatics is an international journal dedicated to methods and tools of computer science and electronic infrastructure applied to biotechnology. The journal covers mainly but not exclusively data/method integration, modeling, simulation and visualization in combination with applications of theoretical/computational tools and any other approach supporting an integrative view of complex biological systems. The final version of this article can be found with all other relevant information at; https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0014/article-10.1515-jib-2020-0014.xml
Uncontrolled Keywords: Diagrams, SBOL visual, Standards
Subjects: Q Science > Q Science (General)
Q Science > QA Mathematics
Q Science > QA Mathematics > QA76 Computer software
T Technology > T Technology (General)
Divisions: Faculty of Natural Sciences > School of Computing and Mathematics
Related URLs:
Depositing User: Symplectic
Date Deposited: 31 Jul 2020 12:53
Last Modified: 31 Jul 2020 12:53
URI: https://eprints.keele.ac.uk/id/eprint/8409

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