Journal of Integrative Bioinformatics (Jun 2020)
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 Goñi,
- 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
Affiliations
- Baig Hasan
- University of Connecticut, Storrs, USA
- Fontanarrosa Pedro
- University of Utah, Salt Lake City, USA
- Kulkarni Vishwesh
- University of Warwick, Coventry, UK
- McLaughlin James
- Newcastle University, Newcastle upon Tyne, UK
- Vaidyanathan Prashant
- Microsoft Research, Cambridge, UK
- Bartley Bryan
- Raytheon BBN Technologies, Cambridge, USA
- Bhatia Swapnil
- Boston University, Boston, USA
- Bhakta Shyam
- Rice University, Houston, USA
- Bissell Michael
- Shipyard Toolchains LLC, Emeryville, USA
- Clancy Kevin
- Thermo Fisher Scientific, San Diego, USA
- Cox Robert Sidney
- Kobe University, Kobe, Japan
- Moreno Angel Goñi
- Newcastle University, Newcastle upon Tyne, UK
- Gorochowski Thomas
- University of Bristol, Bristol, UK
- Grunberg Raik
- KAUST, Thuwal, Saudi Arabia
- Luna Augustin
- Harvard Medical School, Boston, USA
- Madsen Curtis
- Boston University, Boston, USA
- Misirli Goksel
- Keele University, Keele, UK
- Nguyen Tramy
- Raytheon BBN Technologies, Cambridge, USA
- Le Novere Nicolas
- Babraham Institute, Cambridge, UK
- Palchick Zachary
- Zymergen, Emeryville, USA
- Pocock Matthew
- Turing Ate My Hamster, Ltd., Newcastle, UK
- Roehner Nicholas
- Raytheon BBN Technologies, Cambridge, USA
- Sauro Herbert
- University of Washington, Seattle, USA
- Scott-Brown James
- University of Oxford, Oxford, UK
- Sexton John T.
- Rice University, Houston, USA
- Stan Guy-Bart
- Imperial College, London, UK
- Tabor Jeffrey J.
- Rice University, Houston, USA
- Vilar Marta Vazquez
- Universitat Politecnica de Valencia, Valencia, Spain
- Voigt Christopher A.
- MIT, Cambridge, USA
- Wipat Anil
- Newcastle University, Newcastle upon Tyne, UK
- Zong David
- Rice University, Houston, USA
- Zundel Zach
- University of Utah, Salt Lake City, USA
- Beal Jacob
- Raytheon BBN Technologies, Cambridge, USA
- Myers Chris
- University of Utah, Salt Lake City, USA
- DOI
- https://doi.org/10.1515/jib-2020-0014
- Journal volume & issue
-
Vol. 17,
no. 2-3
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.
Keywords
