Abstract
Although many international glycobioinformatics activities have tried to address the challenges of developing informatics to support glycomics analysis, the scope of such an endeavor is huge. Glycomics encompasses the analysis of the glycan complement of prokaryotic and eukaryotic cells and includes free oligosaccharides, glycoproteins, glycolipids, proteoglycans, peptidoglycans, and polysaccharides. As a start to the development of such a knowledge base, we have initially focused on capturing information acquired from glycoproteomics analysis. This chapter outlines the current scope of UniCarbKB (www.unicarbkb.org) to build a curated knowledge base that captures information on glycan structures and accompanying glycoprotein information, inclusive of information pertinent to global and site-specific glycosylation. Access to high-quality data collections will further the development of innovative glycoprotein analysis tools, which will substantially improve our understanding of the roles of glycans and glycoproteins in systems biology.
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References
Aoki-Kinoshita KF (2013) Using databases and web resources for glycomics research. Mol Cell Proteomics 12:1036–1045
Campbell MP, Royle L, Radcliffe CM, Dwek RA, Rudd PM (2008) GlycoBase and autoGU: tools for HPLC-based glycan analysis. Bioinformatics 24:1214–1216
Campbell M, Hayes C, Struwe W, Wilkins M, Aoki-Kinoshita K, Harvey D et al (2011) UniCarbKB: putting the pieces together for glycomics research. Proteomics 11:4117–4121
Campbell M, Ranzinger R, Lutteke T, Mariethoz J, Hayes C, Zhang J et al (2014a) Toolboxes for a standardised and systematic study of glycans. BMC Bioinforma 15:S9
Campbell MP, Peterson R, Mariethoz J, Gasteiger E, Akune Y, Aoki-Kinoshita KF et al (2014b) UniCarbKB: building a knowledge platform for glycoproteomics. Nucleic Acids Res 42:D215–D221
Cooper CA, Harrison MJ, Wilkins MR, Packer NH (2001) GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources. Nucleic Acids Res 29:332–335
Damerell D, Ceroni A, Maass K, Ranzinger R, Dell A, Haslam S (2012) The GlycanBuilder and GlycoWorkbench glycoinformatics tools: updates and new developments. Biol Chem 393:1357–1362
Lutteke T (2008) Web resources for the glycoscientist. Chembiochem 9:2155–2160
Thaysen-Andersen M, Packer NH (2012) Site-specific glycoproteomics confirms that protein structure dictates formation of N-glycan type, core fucosylation and branching. Glycobiology 22:1440–1452
von der Lieth CW, Freire AA, Blank D, Campbell MP, Ceroni A, Damerell DR et al (2011) EUROCarbDB: an open-access platform for glycoinformatics. Glycobiology 21:493–502
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Campbell, M.P., Peterson, R., Gasteiger, E., Mariethoz, J., Lisacek, F., Packer, N.H. (2015). UniCarbKB: Emergent Knowledgebase for Glycomics . In: Taniguchi, N., Endo, T., Hart, G., Seeberger, P., Wong, CH. (eds) Glycoscience: Biology and Medicine. Springer, Tokyo. https://doi.org/10.1007/978-4-431-54841-6_21
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DOI: https://doi.org/10.1007/978-4-431-54841-6_21
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Publisher Name: Springer, Tokyo
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