Madsen Curtis, Goni Moreno Angel, Palchick Zachary, P Umesh, Roehner Nicholas, Bartley Bryan, Bhatia Swapnil, Bhakta Shyam, Bissell Mike, Clancy Kevin, Cox Robert Sidney, Gorochowski Thomas, Grunberg Raik, Luna Augustin, McLaughlin James, Nguyen Tramy, Le Novere Nicolas, Pocock Matthew, Sauro Herbert, Scott-Brown James, Sexton John T, Stan Guy-Bart, Tabor Jeffrey J, Voigt Christopher A, Zundel Zach, Myers Chris, Beal Jacob, Wipat Anil
Boston University, Boston, MA, USA.
Newcastle University, Newcastle, UK.
J Integr Bioinform. 2019 Jun 13;16(2):20180101. doi: 10.1515/jib-2018-0101.
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 2.1 of SBOL Visual, which builds on the prior SBOL Visual 2.0 standard by expanding diagram syntax to include methods for showing modular structure and mappings between elements of a system, interactions arrows that can split or join (with the glyph at the split or join indicating either superposition or a chemical process), and adding new glyphs for indicating genomic context (e.g., integration into a plasmid or genome) and for stop codons.
从事生物有机体工程研究的人员常常发现，用图表进行交流很有用，这些图表既涉及他们正在设计的核酸序列的结构，也涉及序列特征与其他分子种类之间的功能关系。针对此类图表，一些典型的做法和惯例已开始出现。合成生物学开放语言可视化（SBOL Visual）已被开发出来，作为一种标准，用于组织和系统化这些惯例，以便产生一种连贯的语言来表达基因设计的结构和功能。本文详细介绍了SBOL Visual 2.1版本，它在先前的SBOL Visual 2.0标准的基础上进行了扩展，图表语法扩展到包括显示模块化结构和系统元素之间映射的方法、可以拆分或合并的相互作用箭头（在拆分或合并处的符号表示叠加或化学过程），并添加了用于指示基因组背景（例如，整合到质粒或基因组中）和终止密码子的新符号。
