European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
Bioinformatics. 2017 Nov 1;33(21):3461-3467. doi: 10.1093/bioinformatics/btx441.
Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the user to navigate from high level concepts like immune system to detailed pathway diagrams showing biomolecular events like membrane transport or phosphorylation. Here, we present new developments in the Reactome visualization system that facilitate navigation through the pathway hierarchy and enable efficient reuse of Reactome visualizations for users' own research presentations and publications.
For the higher levels of the hierarchy, Reactome now provides scalable, interactive textbook-style diagrams in SVG format, which are also freely downloadable and editable. Repeated diagram elements like 'mitochondrion' or 'receptor' are available as a library of graphic elements. Detailed lower-level diagrams are now downloadable in editable PPTX format as sets of interconnected objects.
Reactome 是一个免费的、开源的、开放数据的、经过精心策划和同行评审的生物分子途径知识库。途径以分层结构排列，该结构在很大程度上对应于 GO 生物学过程层次结构，使用户可以从免疫系统等高级概念导航到详细的途径图，显示膜转运或磷酸化等生物分子事件。在这里，我们介绍了 Reactome 可视化系统的新发展，这些发展有助于通过途径层次结构进行导航，并使用户能够高效地重复使用 Reactome 可视化来进行自己的研究演示和出版物。
对于层次结构的较高层次，Reactome 现在提供可扩展的、交互式的 SVG 格式教科书式图表，这些图表也可以免费下载和编辑。像“线粒体”或“受体”这样的重复图表元素可作为图形元素库使用。详细的低级别的图表现在可以以可编辑的 PPTX 格式下载为相互连接的对象集。
