The MetaboX Library: Building Metabolic Networks from KEGG Database

Motivation In many key applications in the field of metabolomics, such as toxicology or nutrigenomics, it is of interest to profile and detect physiological changes in metabolic pathways. For this purpose, it is useful to build a comprehensive graphical representation which shows metabolic processes occurring in an organism using networks. To model these systems it is possible to describe both reactions and relations among enzymes and metobolites. In this way, analysis of possible changes or perturbations impact throughout the network are easier to understand, detect and predict. To address this problem, we develop a library to build metabolic networks starting from a list of compounds. Results We release the MetaboX library, an open source PHP framework for developing metabolic networks from a set of compounds. This library provides easy access to the Kyoto Encyclopedia for Genes and Genomes (KEGG) database using its RESTful Application Programming Interfaces (APIs), and methods to enhance manipulation of the information returned from KEGG webservice. MetaboX includes methods to extract information about a resource of interest (e.g. metabolite, reaction and enzyme) for further processing and storing purposes. MetaboX is modular, thus developers can contribute with alternative implementations or extensions. Each component of the library is designed with minimum dependency on other components. Supplementary information available in Table 1. Availability The MetaboX library is available under the AGPL license on gitHub repository (https://github.com/Gregmayo/MetaboX-Library)