PathwayBooster: a tool to support the curation of metabolic pathways

BMC Bioinformatics

Rodrigo Liberal¹  Beata K Lisowska²  David J Leak²  John W Pinney¹ 

[1] Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK

[2] Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK

关键词: Metabolic pathways;    Protein function annotation;    Model curation;    Metabolic modelling;   

Others  :  1139034
DOI  :  10.1186/s12859-014-0447-2

 received in 2013-12-04, accepted in 2014-11-03,  发布年份 2015

【 摘 要 】

Background

Despite several recent advances in the automated generation of draft metabolic reconstructions, the manual curation of these networks to produce high quality genome-scale metabolic models remains a labour-intensive and challenging task.

Results

We present PathwayBooster, an open-source software tool to support the manual comparison and curation of metabolic models. It combines gene annotations from GenBank files and other sources with information retrieved from the metabolic databases BRENDA and KEGG to produce a set of pathway diagrams and reports summarising the evidence for the presence of a reaction in a given organism’s metabolic network. By comparing multiple sources of evidence within a common framework, PathwayBooster assists the curator in the identification of likely false positive (misannotated enzyme) and false negative (pathway hole) reactions. Reaction evidence may be taken from alternative annotations of the same genome and/or a set of closely related organisms.

Conclusions

By integrating and visualising evidence from multiple sources, PathwayBooster reduces the manual effort required in the curation of a metabolic model. The software is available online at http://www.theosysbio.bio.ic.ac.uk/resources/pathwaybooster/.

【 授权许可】

   
2015 Liberal et al.; licensee BioMed Central.

【 图 表 】

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【 参考文献 】

• [1]Thiele I, Palsson B: A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 2010, 5:93-121.
• [2]Swainston N, Smallbone K, Mendes P, Kell D, Paton N: The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks. J Integr Bioinform 2011, 8(2):186.
• [3]Henry C, DeJongh M, Best A, Frybarger P, Linsay B, Stevens R: High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 2010, 28(9):977-82.
• [4]Overbeek R, Larsen N, Walunas T, D’Souza M, Pusch G, Selkov E, et al.: The ERGO TM genome analysis and discovery system. Nucleic Acids Res 2003, 31:164-71.
• [5]Orth JD, Thiele I, Palsson BO: What is flux balance analysis? Nat Biotechnol 2010, 28(3):245-8.
• [6]Kim TY, Sohn SB, Kim YB, Kim WJ, Lee SY: Recent advances in reconstruction and applications of genome-scale metabolic models. Curr Opin Biotechnol 2012, 23(4):617-23.
• [7]Liberal R, Pinney J: Simple topological properties predict functional misannotations in a metabolic network. Bioinformatics 2013, 29(13):i154-61.
• [8]Oehm S, Gilbert D, Tauch A, Stoye J, Goesmann A: Comparative Pathway Analyzer: a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Res 2008, 36(suppl 2):W433-7.
• [9]Chou C, Chang W, Chiu C, Huang C, Huang H: FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Res 2009, 37(suppl 2):W129-34.
• [10]Choi K, Kim S: ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts. BMC Bioinformatics 2008, 9:145. BioMed Central Full Text
• [11]Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A: UniProtKB/Swiss-Prot. Database 2007, 2:3.
• [12]Lee T, Huang H, Hung J, Huang H, Yang Y, Wang T: dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res 2006, 34(suppl 1):D622-7.
• [13]Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, et al.: BRENDA, the enzyme information system in 2011. Nucleic Acids Res 2011, 39(suppl 1):D670-6.
• [14]Tatusov R, Koonin E, Lipman D: A genomic perspective on protein families. Science 1997, 278(5338):631-7.
• [15]Altschul S, Gish W, Miller W, Myers E, Lipman D: Basic local alignment search tool. J Mol Biol 1990, 215(3):403-10.
• [16]Ashida H, Saito Y, Kojima C, Yokota A: Enzymatic characterization of 5-methylthioribulose-1-phosphate dehydratase of the methionine salvage pathway in Bacillus subtilis. Biosci Biotechnol Biochem 2008, 72(4):959-67.
• [17]Pabinger S, Rader R, Agren R, Nielsen J, Trajanoski Z: MEMOSysBioinformatics platform for genome-scale metabolic models. BMC Syst Biol 2011, 5:20. BioMed Central Full Text
• [18]Liao Y, Tsai M, Chen F, Hsiung C: GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization. Bioinformatics 2012, 28(13):1752-8.