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 URLanism 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 URL
 In many key applications of metabolomics, such as toxicology or nutrigenomics, it is of interest to profile and detect changes in metabolic processes, usually represented in the form of pathways. As an alternative, a broader point of view would enable investigators to better understand the relations between entities that exist in different processes. Therefore, relating a possible perturbation to several known processes represents a new approach to this field of study. We propose to use a network representation of metabolism in terms of reactants, enzyme and metabolite . To model these systems it is possible to describe both reactions and relations among enzymes and metabolites . In this way, analysis of the impact of changes in some metabolites or enzymes on different processes are easier to understand, detect and predict. Results: We release the MetaboX library, an open source PHP framework for developing metabolic networks from a set of compounds. This library uses data stored in 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. The MetaboX library includes methods to extract information about a resource of interest (e.g. metabolite, reaction and enzyme) and to build reactants networks, bipartite enzyme-metabolite and unipartite enzyme networks. These networks can be exported in different formats for data visualization with standard tools. As a case study, the networks built from a subset of the Glycolysis pathway are described and discussed. Conclusions: The advantages of using such a library imply the ability to model complex systems with few starting information represented by a collection of metabolites KEGG IDs.
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Motivation
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in the field
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physiological
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pathways
processes, usually represented in the form of pathways. As an alternative, a broader point of view would enable investigators to better understand the relations between entities that exist in different processes. Therefore, relating a possible perturbation to several known processes represents a new approach to this field of study. We propose to use a network representation of metabolism in terms of reactants, enzyme and metabolite
D
For this purpose, it is useful to build a comprehensive graphical representation which shows metabolic processes occurring in URLanism using networks.
R
metobolites
metabolites
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possible changes or perturbations impact throughout the network
the impact of changes in some metabolites or enzymes on different processes
R
To address this problem, we develop a library to build metabolic networks starting from a list of compounds. Results
Results:
R
provides easy access to the
uses data stored in
R
MetaboX
The MetaboX library
R
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 URL
and to build reactants networks, bipartite enzyme-metabolite and unipartite enzyme networks. These networks can be exported in different formats for data visualization with standard tools. As a case study, the networks built from a subset of the Glycolysis pathway are described and discussed. Conclusions: The advantages of using such a library imply the ability to model complex systems with few starting information represented by a collection of metabolites KEGG IDs.