ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases
ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases
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DOI：
10.1038/s41540-018-0078
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发表时间：
2018-12-13
影响因子：
4
通讯作者：
Hofmann-Apitius, Martin
中科院分区：
文献类型：
--
作者：
Domingo-Fernandez, Daniel;Hoyt, Charles Tapley;Hofmann-Apitius, Martin
尽管路径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，缺乏互操作性，阻碍了对它们之间的覆盖范围、协议和差异的评估。在这里，我们介绍了ComPath，这是一个支持数据库之间路径映射管理的生态系统，并通过几种新颖的可视化方法促进了路径知识的探索。我们整理了三个主要通路数据库之间的映射，并提出了一个以帕金森病为重点的案例研究，说明了ComPath如何通过识别这些映射的通路模块、簇和交叉对话来产生新的生物学见解。ComPath源代码和资源可在https://github.com/ComPath上获得，web应用程序可在https://compath.scai.fraunhofer.de/上访问。
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/.