Gauges Ralph, Rost Ursula, Sahle Sven, Wengler Katja, Bergmann Frank Thomas
J Integr Bioinform. 2015 Sep 4;12(2):267. doi: 10.2390/biecoll-jib-2015-267.
Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). For software tools that also read and write models in SBML (Systems Biology Markup Language) format, a common need is to store the network diagram together with the SBML representation of the model. This in turn raises the question of how to encode the layout and the rendering of these diagrams. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding diagrams, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The Layout package for SBML Level 3 adds the necessary features to SBML so that diagram layouts can be encoded in SBML files, and a companion package called SBML Rendering specifies how the graphical rendering of elements can be encoded. The SBML Layout package is based on the principle that reaction network diagrams should be described as representations of entities such as species and reactions (with direct links to the underlying SBML elements), and not as arbitrary drawings or graphs; for this reason, existing languages for the description of vector drawings (such as SVG) or general graphs (such as GraphML) cannot be used.
许多软件工具提供了以可视化形式描绘反应网络图的功能。这种可视化图的两个方面可以区分：图中元素的布局（即：定位和连接），以及元素的图形形式（例如，用于符号的字形、连接它们的线条的属性等等）。对于也以SBML（系统生物学标记语言）格式读取和写入模型的软件工具，一个常见的需求是将网络图与模型的SBML表示一起存储。这反过来又引发了如何对这些图的布局和渲染进行编码的问题。SBML Level 3版本1核心规范没有提供显式编码图的机制，但它确实提供了一种机制，使SBML包能够扩展核心规范并添加额外的语法结构。SBML Level 3的布局包为SBML添加了必要的功能，以便可以在SBML文件中编码图布局，并且一个名为SBML渲染的配套包指定了如何对元素的图形渲染进行编码。SBML布局包基于这样的原则：反应网络图应该被描述为诸如物种和反应等实体的表示（与底层的SBML元素有直接链接），而不是任意的绘图或图形；因此，不能使用现有的用于描述矢量绘图（如SVG）或通用图形（如GraphML）的语言。
