A Practical Guide to Using Glycomics Databases

This book provides glycoscientists with a handbook of useful databases that can be applied to glycoscience research. Although many databases are now publicly available, one of the hurdles for their users is the learning curve required to effectively utilize those databases. Therefore, this book not only describes the existing databases, but also provides tips on how to obtain the target data. That is, because many databases provide a variety of data that could be obtained from different perspectives, each chapter provides users with potential biological questions that can be answered by a particular database and step-by-step instructions, with figures, on how to obtain that data. Troubleshooting tips are also provided to aid users encountering problems that can be predicted when using these databases. Moreover, contact information for each database is provided in case unexpected issues arise.

• Development of Carbohydrate Nomenclature and Representation, S. Perez, et al.
• Translation and Validation of Carbohydrate Residue Names with MonosaccharideDB Routines, T. Lütteke
• Using GlyTouCan Version 1.0 : The First International Glycan Structure Repository, D. Shinmachi, et al.
• Carbohydrate Structure Database (CSDB) : Examples of Usage, K.S. Egorova, et al.
• The CAZy Database/the Carbohydrate-Active Enzyme (CAZy) Database : Principles and Usage Guidelines, N. Terrapon, Nicolas, et al.
• Glyco3D : A Suite of Interlinked Databases of 3D Structures of Complex Carbohydrates, Lectins, Antibodies, and Glycosyltransferases, S. Pérez, et al.
• GlycoGene Database (GGDB) on the Semantic Web, H. Narimatsu, Hisashi, et al.
• KEGG GLYCAN , M. Kanehisa
• Exploring the UniCarbKB Database, M.P. Campbell, et al.
• GlycoProtDB : A Database of Glycoproteins Mapped with Actual Glycosylation Sites Identified by Mass Spectrometry, H. Kaji, et al.
• GlycoEpitope, S. Okuda, et al.
• SugarBindDB, J. Mariethoz, et al.
• PAConto : RDF Representation of PACDB Data and Ontology of Infectious Diseases Known to Be Related to Glycan Binding, E. Solovieva, et al.
• RINGS : A Web Resource of Tools for Analyzing Glycomics Data, K.F. Aoki-Kinoshita
• Glycan Data Retrieval and Analysis Using GLYCOSCIENCES.de Applications, T. Lütteke
• Glycobiology Meets the Semantic Web, S. Kawano