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A Practical Guide to Using Glycomics Databases

  • Book
  • © 2017

Overview

Editors:
  1. Kiyoko F. Aoki-Kinoshita

    1. Faculty of Science and Engineering, Soka University, Hachioji, Japan

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  • Gives step-by-step instructions on how to use each database to obtain a particular objective, helping readers to quickly learn to use the relevant database for their research

  • Is written by the developers themselves, describing in detail the features that are unique to each database

  • Presents troubleshooting tips to explain issues that may commonly be faced by users

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Table of contents (17 chapters)

  1. Front Matter

    Pages i-ix
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  2. Introduction

    1. Front Matter

      Pages 1-1
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    2. Introduction

      • Nicolle H. Packer
      Pages 3-5

    3. Development of Carbohydrate Nomenclature and Representation

      • Serge Perez, Kiyoko F. Aoki-Kinoshita
      Pages 7-25

  3. Monosaccharide and Glycan Structures

    1. Front Matter

      Pages 27-27
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    2. Translation and Validation of Carbohydrate Residue Names with MonosaccharideDB Routines

      • Thomas Lütteke
      Pages 29-40

    3. Using GlyTouCan Version 1.0: The First International Glycan Structure Repository

      • Daisuke Shinmachi, Issaku Yamada, Nobuyuki P. Aoki, Masaaki Matsubara, Kiyoko F. Aoki-Kinoshita, Hisashi Narimatsu
      Pages 41-73

    4. Carbohydrate Structure Database (CSDB): Examples of Usage

      • Ksenia S. Egorova, Philip V. Toukach
      Pages 75-113

  4. Glyco-related Genes and Proteins

    1. Front Matter

      Pages 115-115
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    2. The CAZy Database/the Carbohydrate-Active Enzyme (CAZy) Database: Principles and Usage Guidelines

      • Nicolas Terrapon, Vincent Lombard, Elodie Drula, Pedro M. Coutinho, Bernard Henrissat
      Pages 117-131

    3. Glyco3D: A Suite of Interlinked Databases of 3D Structures of Complex Carbohydrates, Lectins, Antibodies, and Glycosyltransferases

      • Serge Pérez, Anita Sarkar, Alain Rivet, Sophie Drouillard, Christelle Breton, Anne Imberty
      Pages 133-161

    4. GlycoGene Database (GGDB) on the Semantic Web

      • Hisashi Narimatsu, Yoshinori Suzuki, Kiyoko F. Aoki-Kinoshita, Noriaki Fujita, Hiromichi Sawaki, Toshihide Shikanai et al.
      Pages 163-175

    5. KEGG GLYCAN

      • Minoru Kanehisa
      Pages 177-193

  5. Glycoproteomics Data

    1. Front Matter

      Pages 195-195
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    2. Exploring the UniCarbKB Database

      • Matthew P. Campbell, Robyn A. Peterson, Elisabeth Gasteiger, Frederique Lisacek, Nicolle H. Packer
      Pages 197-214

    3. GlycoProtDB: A Database of Glycoproteins Mapped with Actual Glycosylation Sites Identified by Mass Spectrometry

      • Hiroyuki Kaji, Toshihide Shikanai, Yoshinori Suzuki, Hisashi Narimatsu
      Pages 215-224

  6. Glycan Interactions

    1. Front Matter

      Pages 225-225
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    2. GlycoEpitope

      • Shujiro Okuda, Hiromi Nakao, Toshisuke Kawasaki
      Pages 227-245

    3. SugarBindDB

      • Julien Mariethoz, Khaled Khatib, Tiphaine Mannic, Davide Alocci, Matthew P. Campbell, Nicolle H. Packer et al.
      Pages 247-260

    4. PAConto: RDF Representation of PACDB Data and Ontology of Infectious Diseases Known to Be Related to Glycan Binding

      • Elena Solovieva, Noriaki Fujita, Toshihide Shikanai, Kiyoko F. Aoki-Kinoshita, Hisashi Narimatsu
      Pages 261-295
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Keywords

About this book

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.

Editors and Affiliations

  • Faculty of Science and Engineering, Soka University, Hachioji, Japan

    Kiyoko F. Aoki-Kinoshita

About the editor

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

Bibliographic Information

  • Book Title: A Practical Guide to Using Glycomics Databases

  • Editors: Kiyoko F. Aoki-Kinoshita

  • DOI: https://doi.org/10.1007/978-4-431-56454-6

  • Publisher: Springer Tokyo

  • eBook Packages: Biomedical and Life Sciences, Biomedical and Life Sciences (R0)

  • Copyright Information: Springer Japan 2017

  • Hardcover ISBN: 978-4-431-56452-2Published: 12 January 2017

  • Softcover ISBN: 978-4-431-56790-5Published: 07 July 2018

  • eBook ISBN: 978-4-431-56454-6Published: 06 December 2016

  • Edition Number: 1

  • Number of Pages: IX, 370

  • Number of Illustrations: 48 b/w illustrations, 178 illustrations in colour

  • Topics: Bioinformatics, Proteomics

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