Journal article
Synthetic biology open language visual (SBOL visual) version 2.2
Journal of integrative bioinformatics, Vol.17(2-3), 20200014
06/10/2020
DOI: 10.1515/jib-2020-0014
PMCID: PMC7756616
PMID: 32543457
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.
Details
- Title: Subtitle
- Synthetic biology open language visual (SBOL visual) version 2.2
- Creators
- Hasan Baig - University of ConnecticutPedro Fontanarrosa - University of UtahVishwesh Kulkarni - University of WarwickJames McLaughlin - Newcastle UniversityPrashant Vaidyanathan - Microsoft ResearchBryan Bartley - RTXSwapnil Bhatia - Boston UniversityShyam Bhakta - Rice UniversityMichael Bissell - Shipyard Toolchains LLC, Emeryville, CA USAKevin Clancy - Thermo Fisher ScientificRobert Sidney Cox - Kobe UniversityAngel Goni Moreno - Newcastle UniversityThomas Gorochowski - University of BristolRaik Grunberg - King Abdullah University of Science and TechnologyAugustin Luna - Harvard UniversityCurtis Madsen - Boston UniversityGoksel Misirli - Keele UniversityTramy Nguyen - RTXNicolas Le Novere - Babraham InstituteZachary Palchick - ZogenixMatthew Pocock - Turing InstituteNicholas Roehner - RTXHerbert Sauro - University of WashingtonJames Scott-Brown - University of OxfordJohn T. Sexton - Rice UniversityGuy-Bart Stan - Imperial Coll, London, EnglandJeffrey J. Tabor - Rice UniversityMarta Vazquez Vilar - Univ Politecn Valencia, Valencia, SpainChristopher A. Voigt - IIT@MITAnil Wipat - Newcastle UniversityDavid Zong - Rice UniversityZach Zundel - University of UtahJacob Beal - RTXChris Myers - University of Utah
- Resource Type
- Journal article
- Publication Details
- Journal of integrative bioinformatics, Vol.17(2-3), 20200014
- Publisher
- Walter De Gruyter
- DOI
- 10.1515/jib-2020-0014
- PMID
- 32543457
- PMCID
- PMC7756616
- ISSN
- 1613-4516
- eISSN
- 1613-4516
- Number of pages
- 85
- Grant note
- BBS/E/B/000C0434 / BBSRC; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC)
- Language
- English
- Date published
- 06/10/2020
- Academic Unit
- Electrical and Computer Engineering
- Record Identifier
- 9984627299602771
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