University of Connecticut, Storrs, USA.
University of Utah, Salt Lake City, USA.
J Integr Bioinform. 2021 Oct 20;18(3):20210013. doi: 10.1515/jib-2021-0013.
People who engineer biological organisms often find it useful to draw diagrams in order to communicate both the structure of the nucleic acid sequences that they are engineering and the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 3.0 of SBOL Visual, a new major revision of the standard. The major difference between SBOL Visual 3 and SBOL Visual 2 is that diagrams and glyphs are defined with respect to the SBOL 3 data model rather than the SBOL 2 data model. A byproduct of this change is that the use of dashed undirected lines for subsystem mappings has been removed, pending future determination on how to represent general SBOL 3 constraints; in the interim, this annotation can still be used as an annotation. Finally, deprecated material has been removed from collection of glyphs: the deprecated "insulator" glyph and "macromolecule" alternative glyphs have been removed, as have the deprecated BioPAX alternatives to SBO terms.
设计生物有机体的工程师经常发现，为了传达他们正在设计的核酸序列的结构以及序列特征与其他分子种类之间的功能关系，绘制图表是很有用的。对于这样的图表，一些典型的实践和惯例已经开始出现。SBOL Visual 的目的是组织和系统化这些惯例，以便为表达遗传设计的结构和功能提供一个连贯的语言。本文详细介绍了 SBOL Visual 的 3.0 版本，这是该标准的一个重大修订。SBOL Visual 3 与 SBOL Visual 2 的主要区别在于，图表和符号是根据 SBOL 3 数据模型而不是 SBOL 2 数据模型定义的。这一变化的一个结果是，用于子系统映射的虚线无向线已被删除，等待未来确定如何表示一般的 SBOL 3 约束；在此期间，仍然可以将此注释用作注释。最后，从符号集合中删除了已弃用的材料：已删除已弃用的“绝缘体”符号和“大分子”替代符号，以及已弃用的 BioPAX 对 SBO 术语的替代。
