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Critical assessment of genome-scale metabolic networks: The need for a unified standard
Aarthi Ravikrishnan,
Published in Oxford University Press
PMID: 25725218
Volume: 16
Issue: 6
Pages: 1057 - 1068
Genome-scale metabolic networks have been reconstructed for several organisms. These metabolic networks provide detailed information about the metabolisminside the cells, coupled with the genomic, proteomic and thermodynamic information. These networks are widely simulated using 'constraint-based' modelling techniques and find applications ranging from strain improvement for metabolic engineering to prediction of drug targets in pathogenic organisms. Components of these metabolic networks are represented in multiple file formats and also using different markup languages, with varying levels of annotations; this leads to inconsistencies and increases the complexities in comparing and analysing reconstructions on multiple platforms. In this work, we critically examine nearly 100 published genome-scale metabolic networks and their corresponding constraint-based models and discuss various issues with respect to model quality. One of the major concerns is the lack of annotations using standard identifiers that can uniquely describe several components such as metabolites, genes, proteins and reactions. We also find that many models do not have complete information regarding constraints on reactions fluxes and objective functions for carrying out simulations. Overall, our analysis highlights the need for a widely acceptable standard for representing constraint-based models. A rigorous standard can help in streamlining the process of reconstruction and improve the quality of reconstructed metabolic models. © The Author 2015. Published by Oxford University Press.
About the journal
JournalData powered by TypesetBriefings in Bioinformatics
PublisherData powered by TypesetOxford University Press
Open AccessNo
Concepts (4)
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    Theoretical model
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    Models, theoretical