Roehner Nicholas, Oberortner Ernst, Pocock Matthew, Beal Jacob, Clancy Kevin, Madsen Curtis, Misirli Goksel, Wipat Anil, Sauro Herbert, Myers Chris J
Department of Bioengineering, University of Utah , Salt Lake City, Utah, United States.
ACS Synth Biol. 2015 Jan 16;4(1):57-71. doi: 10.1021/sb500176h. Epub 2014 Jun 16.
While the first version of the Synthetic Biology Open Language (SBOL) has been adopted by several academic and commercial genetic design automation (GDA) software tools, it only covers a limited number of the requirements for a standardized exchange format for synthetic biology. In particular, SBOL Version 1.1 is capable of representing DNA components and their hierarchical composition via sequence annotations. This proposal revises SBOL Version 1.1, enabling the representation of a wider range of components with and without sequences, including RNA components, protein components, small molecules, and molecular complexes. It also introduces modules to instantiate groups of components on the basis of their shared function and assert molecular interactions between components. By increasing the range of structural and functional descriptions in SBOL and allowing for their composition, the proposed improvements enable SBOL to represent and facilitate the exchange of a broader class of genetic designs.
虽然合成生物学开放语言（SBOL）的第一版已被多个学术和商业基因设计自动化（GDA）软件工具采用，但它仅涵盖了合成生物学标准化交换格式的有限数量的要求。特别是，SBOL版本1.1能够通过序列注释来表示DNA组件及其层次结构组成。本提案对SBOL版本1.1进行了修订，使得能够表示更多带有或不带有序列的组件，包括RNA组件、蛋白质组件、小分子和分子复合物。它还引入了模块，以便根据组件的共享功能实例化组件组，并断言组件之间的分子相互作用。通过增加SBOL中结构和功能描述的范围并允许其组合，所提出的改进使SBOL能够表示并促进更广泛类别的基因设计的交换。
