1Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754 Sankt Augustin, Germany.
2Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany.
NPJ Syst Biol Appl. 2018 Dec 13;5:3. doi: 10.1038/s41540-018-0078-8. eCollection 2019.
Although pathways are widely used for the analysis and representation of biological systems, their lack of clear boundaries, their dispersion across numerous databases, and the lack of interoperability impedes the evaluation of the coverage, agreements, and discrepancies between them. Here, we present ComPath, an ecosystem that supports curation of pathway mappings between databases and fosters the exploration of pathway knowledge through several novel visualizations. We have curated mappings between three of the major pathway databases and present a case study focusing on Parkinson's disease that illustrates how ComPath can generate new biological insights by identifying pathway modules, clusters, and cross-talks with these mappings. The ComPath source code and resources are available at https://github.com/ComPath and the web application can be accessed at https://compath.scai.fraunhofer.de/.
虽然通路被广泛用于生物系统的分析和表示，但它们缺乏明确的边界、分散在众多数据库中，以及缺乏互操作性，这些都阻碍了对它们之间的覆盖范围、一致性和差异的评估。在这里，我们提出了 ComPath，这是一个支持数据库之间通路映射策展的生态系统，并通过几种新颖的可视化方法促进了对通路知识的探索。我们已经在三个主要的通路数据库之间策展了映射，并提出了一个聚焦帕金森病的案例研究，说明了 ComPath 如何通过识别通路模块、聚类以及与这些映射的交叉对话，来生成新的生物学见解。ComPath 的源代码和资源可在 https://github.com/ComPath 上获得，该网络应用程序可在 https://compath.scai.fraunhofer.de/ 上访问。
