Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan.
Com. Bio Big Data Open Innovation Lab. (CBBD-OIL), AIST, Aomi, Tokyo, Japan.
Bioinformatics. 2019 Nov 1;35(21):4499-4500. doi: 10.1093/bioinformatics/btz287.
The systems biology graphical notation (SBGN) has emerged as the main standard to represent biological maps graphically. It comprises three complementary languages: Process Description, for detailed biomolecular processes; Activity Flow, for influences of biological activities and Entity Relationship, for independent relations shared among biological entities. On the other hand, TikZ is one of the most commonly used package to 'program' graphics within TEX/LATEX. Here, we present sbgntikz, a TikZ library that allows drawing and customizing SBGN maps directly into TEX/LATEX documents, using the TikZ language. sbgntikz supports all glyphs of the three SBGN languages, and offers options that facilitate the drawing of complex glyph assembly within TikZ. Furthermore, sbgntikz is provided together with a converter that allows transforming any SBGN map stored under the SBGN Markup Language into a TikZ picture, or rendering it directly into a PDF file.
sbgntikz, the SBGN-ML to sbgntikz converter, as well as a complete documentation can be freely downloaded from https://github.com/Adrienrougny/sbgntikz/. The library and the converter are compatible with all recent operating systems, including Windows, MacOS, and all common Linux distributions.
Supplementary material is available at Bioinformatics online.
系统生物学图形符号 (SBGN) 已经成为图形表示生物图谱的主要标准。它包括三种互补的语言：过程描述，用于详细的生物分子过程；活动流，用于生物活动的影响；实体关系，用于生物实体之间共享的独立关系。另一方面，TikZ 是 TEX/LATEX 中最常用的“编程”图形的包之一。在这里，我们介绍了 sbgntikz，这是一个 TikZ 库，允许使用 TikZ 语言直接在 TEX/LATEX 文档中绘制和自定义 SBGN 图谱。sbgntikz 支持三个 SBGN 语言的所有符号，并提供了一些选项，可简化在 TikZ 中绘制复杂符号组合。此外，sbgntikz 还提供了一个转换器，可以将任何以 SBGN 标记语言存储的 SBGN 图谱转换为 TikZ 图片，或者直接将其渲染为 PDF 文件。
sbgntikz、SBGN-ML 到 sbgntikz 的转换器以及完整的文档可以从 https://github.com/Adrienrougny/sbgntikz/ 免费下载。该库和转换器与所有最新的操作系统兼容，包括 Windows、MacOS 和所有常见的 Linux 发行版。
补充材料可在 Bioinformatics 在线获得。
