Rougny Adrien, Touré Vasundra, Moodie Stuart, Balaur Irina, Czauderna Tobias, Borlinghaus Hanna, Dogrusoz Ugur, Mazein Alexander, Dräger Andreas, Blinov Michael L, Villéger Alice, Haw Robin, Demir Emek, Mi Huaiyu, Sorokin Anatoly, Schreiber Falk, Luna Augustin
Biotechnology Research Institute for Drug Discovery, AIST, Tokyo135-0064, Japan.
Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo 169-8555, Japan.
J Integr Bioinform. 2019 Jun 13;16(2):20190022. doi: 10.1515/jib-2019-0022.
The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support an efficient and accurate exchange of biological knowledge between disparate research communities, industry, and other players in systems biology. SBGN comprises the three languages Entity Relationship, Activity Flow, and Process Description (PD) to cover biological and biochemical systems at distinct levels of detail. PD is closest to metabolic and regulatory pathways found in biological literature and textbooks. Its well-defined semantics offer a superior precision in expressing biological knowledge. PD represents mechanistic and temporal dependencies of biological interactions and transformations as a graph. Its different types of nodes include entity pools (e.g. metabolites, proteins, genes and complexes) and processes (e.g. reactions, associations and influences). The edges describe relationships between the nodes (e.g. consumption, production, stimulation and inhibition). This document details Level 1 Version 2.0 of the PD specification, including several improvements, in particular: 1) the addition of the equivalence operator, subunit, and annotation glyphs, 2) modification to the usage of submaps, and 3) updates to clarify the use of various glyphs (i.e. multimer, empty set, and state variable).
系统生物学图形符号（SBGN）是一项国际社会共同努力的成果，旨在为具有不同科学背景的读者规范途径和网络的可视化表示，同时支持不同研究群体、行业以及系统生物学中的其他参与者之间高效、准确地交流生物学知识。SBGN包含实体关系、活动流和过程描述（PD）这三种语言，以涵盖不同详细程度的生物和生化系统。PD与生物学文献和教科书中的代谢途径和调节途径最为接近。其明确的语义在表达生物学知识方面具有更高的精度。PD将生物相互作用和转化的机制及时间依赖性表示为一个图形。它的不同类型节点包括实体池（如代谢物、蛋白质、基因和复合物）和过程（如反应、关联和影响）。边描述节点之间的关系（如消耗、产生、刺激和抑制）。本文详细介绍了PD规范的1.0版本2.0，包括一些改进，特别是：1）添加了等价运算符、亚基和注释符号；2）修改了子图的用法；3）更新内容以明确各种符号（即多聚体、空集和状态变量）的使用。
