A Practical Guide to Using Glycomics Databases

Kiyoko F. Aoki-Kinoshita Associate Professor, Department of Bioinformatics, Faculty of Engineering, Soka University, 1–236 Tangi-machi, Hachioji, Tokyo, 192–8577 Japan

Preface.- Part I Introduction.- Chapter1 Introduction.- Chapter2 Development of Carbohydrate Nomenclature and Representation.- Part II Monosaccharide and glycan structures.- Chapter 3 Translation and validation of carbohydrate residue names with MonosaccharideDB routines.- Chapter4 Using GlyTouCan version 1.0: The first international glycan structure repository.- Chapter5 CARBOHYDRATE STRUCTURE DATABASE (CSDB) – examples of usage.- Part III Glyco-related genes and proteins.- Chapter6 The CAZy Database / The Carbohydrate-Active Enzyme (CAZy) database: principles and usage guidelines.- Chapter7 Glyco3D: A Suite of Inter-linked Databases of 3D Structures of Complex Carbohydrates, Lectins, Antibodies and Glycosyltransferases.- Chapter8 GlycoGene Database (GGDB) on the Semantic Web.- Chapter9 KEGG GLYCAN Database.- Part IV Glycoproteomics data.- Chapter10 Exploring the UniCarbKB Database.- Chapter11 GlycoProtDB –A database of glycoproteins mapped with actual glycosylation sites identified by mass spectrometry.- Part V Glycan interactions.- Chapter12 GlycoEpitope.- Chapter13 SugarBindDB.- Chapter14 PAConto - RDF representation of PACDB data and Ontology of Infectious Diseases known to be related to Glycan Binding.- Part VI Glycan data analysis.- Chapter15 RINGS: a web resource of tools for analyzing glycomics data.- Chapter16 Glycan data retrieval and analysis using GLYCOSCIENCES.de applications.- Chapter17 Glycobiology meets the Semantic Web.