Madsen Curtis, Goñi Moreno Angel, P Umesh, Palchick Zachary, Roehner Nicholas, Atallah Christian, Bartley Bryan, Choi Kiri, Cox Robert Sidney, Gorochowski Thomas, Grünberg Raik, Macklin Chris, McLaughlin James, Meng Xianwei, Nguyen Tramy, Pocock Matthew, Samineni Meher, Scott-Brown James, Tarter Ysis, Zhang Michael, Zhang Zhen, Zundel Zach, Beal Jacob, Bissell Michael, Clancy Kevin, Gennari John H, Misirli Goksel, Myers Chris, Oberortner Ernst, Sauro Herbert, Wipat Anil
Boston University, Boston, MA, USA.
Newcastle University, Newcastle, UK.
J Integr Bioinform. 2019 Jun 13;16(2):20190025. doi: 10.1515/jib-2019-0025.
Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems is to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.3.0 of SBOL, which builds upon version 2.2.0 published in last year's JIB Standards in Systems Biology special issue. In particular, SBOL 2.3.0 includes means of succinctly representing sequence modifications, such as insertion, deletion, and replacement, an extension to support organization and attachment of experimental data derived from designs, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, refinement of a number of validation rules, improved figures and examples, and clarification on a number of issues related to the use of external ontology terms.
合成生物学通过将工程原理应用于生物系统设计，建立在遗传学、分子生物学和代谢工程的技术及成果之上。该领域仍面临诸多重大挑战，包括开发时间长、失败率高和可重复性差等问题。改善这些问题的一种方法是加强实验室之间关于设计系统的信息交流。合成生物学开放语言（SBOL）已被开发为一种标准，以支持合成生物学中生物设计信息的规范和交换，满足了其他现有标准未满足的需求。本文详细介绍了SBOL 2.3.0版本，它基于去年发表在《系统生物学杂志》标准专刊上的2.2.0版本构建。特别是，SBOL 2.3.0包括简洁表示序列修饰（如插入、缺失和替换）的方法、支持组织和附加源自设计的实验数据的扩展，以及用于描述设计元件数值参数的扩展。新版本还包括指定合成生物学活动的类型、具有多种编码的序列的明确位置、若干验证规则的细化、改进的图表和示例，以及对与使用外部本体术语相关的若干问题的澄清。
