ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases.,npj Systems Biology and Applications

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ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases.
npj Systems Biology and Applications ( IF 3.5 ) Pub Date : 2018-12-13 , DOI: 10.1038/s41540-018-0078-8
Daniel Domingo-Fernández _{1,

2} , Charles Tapley Hoyt _{1,

2} , Carlos Bobis-Álvarez ₃ , Josep Marín-Llaó _{1,

4} , Martin Hofmann-Apitius _{1,

2}

Affiliation

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/.

中文翻译：

ComPath：一个用于探索，分析和管理跨途径数据库映射的生态系统。

尽管途径被广泛用于生物系统的分析和表示，但是它们缺乏明确的边界，它们在众多数据库中的分散性以及缺乏互操作性阻碍了对其范围，协议和差异的评估。在这里，我们介绍ComPath，这是一个生态系统，可支持数据库之间路径映射的管理，并通过几种新颖的可视化方法促进对路径知识的探索。我们已经整理了三个主要途径数据库之间的映射，并针对帕金森氏病进行了案例研究，该案例研究说明了ComPath如何通过识别这些映射的途径模块，簇和串扰来产生新的生物学见解。可在https：// github上找到ComPath源代码和资源。

更新日期：2018-12-13

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