Comparative Analysis of Biochemical Network Reconstructions

Abstract

Reconstruction of genome-scale metabolic network is a result of assembling various information sources about all biochemical reactions expected in the metabolic network of interest. Despite the efforts of leading bio-models databases to make comparison of biochemical networks by elements names obsolete, interest from researchers in using string similarity metrics in comparison of metabolites names has been growing. Multiple challenges in comparison of reconstructions are discussed in this article and an insight into current approach of metabolic model comparison has been given. The discussion of challenges and attempts to solve them are followed by the author’s proposed algorithm for models comparison that can be particularly useful in case of reconstructions. Special attention is given to the use of metabolites names and chemical formulas. The author’s proposed algorithm has been implemented in a software tool ModeRator. The article is concluded with use cases of the comparison algorithm and the software tool.