Jun 21, 2018

ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases

BioRxiv : the Preprint Server for Biology
Daniel Domingo-FernandezMartin Hofmann-Apitius

Abstract

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 http://compath.scai.fraunhofer.de/

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Mentioned in this Paper

Biochemical Pathway
Cross-talk
Evaluation
Parkinson Disease
Analysis
Gene Clusters
SCAI gene
Case-Control Studies
Dispersion
Parkinson's Disease Pathway

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