Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan.
The Donnelly Centre, University of Toronto, M5S 3E1, Toronto, Canada.
Brief Bioinform. 2021 Sep 2;22(5). doi: 10.1093/bib/bbab049.
A comprehensible representation of a molecular network is key to communicating and understanding scientific results in systems biology. The Systems Biology Graphical Notation (SBGN) has emerged as the main standard to represent such networks graphically. It has been implemented by different software tools, and is now largely used to communicate maps in scientific publications. However, learning the standard, and using it to build large maps, can be tedious. Moreover, SBGN maps are not grounded on a formal semantic layer and therefore do not enable formal analysis. Here, we introduce a new set of patterns representing recurring concepts encountered in molecular networks, called SBGN bricks. The bricks are structured in a new ontology, the Bricks Ontology (BKO), to define clear semantics for each of the biological concepts they represent. We show the usefulness of the bricks and BKO for both the template-based construction and the semantic annotation of molecular networks. The SBGN bricks and BKO can be freely explored and downloaded at sbgnbricks.org.
分子网络的可理解表示是在系统生物学中进行科学交流和理解的关键。系统生物学图形符号（SBGN）已经成为图形表示此类网络的主要标准。它已经被不同的软件工具实现，并且现在被广泛用于在科学出版物中交流图谱。然而，学习该标准并使用它来构建大型图谱可能很繁琐。此外，SBGN 图谱没有基于正式的语义层，因此不能进行形式分析。在这里，我们引入了一组新的模式，用于表示在分子网络中遇到的重复概念，称为 SBGN 积木。这些积木被组织在一个新的本体中，称为 Bricks Ontology（BKO），为它们所表示的每个生物学概念定义明确的语义。我们展示了积木和 BKO 在基于模板的构建和分子网络的语义注释中的有用性。SBGN 积木和 BKO 可以在 sbgnbricks.org 上自由探索和下载。
