Skip to main content
SpringerLink
Log in

GlycomeDB

  • Protocol
  • First Online:
Glycoinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1273))

Abstract

Over the last two decades, several carbohydrate structure databases have been developed and made publicly available by different research groups around the world. This led to the fragmentation of information about carbohydrate structures into different resources that have no or only weak interaction with each other. GlycomeDB was developed to integrate the carbohydrate structures from different resources by generating a single-indexed catalog of these structures that associates each structure with its reference in the original resources.

GlycomeDB facilitates searching for carbohydrate structures in all the integrated resources by eliminating the need to use several different search interfaces and manually integrating the results. References provided by GlycomeDB make it possible to retrieve information that is beyond the scope of GlycomeDB but present in the integrated databases. This chapter illustrates the use of the GlycomeDB search interfaces and web services by way of three example cases.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Doubet S, Albersheim P (1992) CarbBank. Glycobiology 2:505

    Article  CAS  PubMed  Google Scholar 

  2. Doubet S, Bock K, Smith D, Darvill A, Albersheim P (1989) The complex carbohydrate structure database. Trends Biochem Sci 14:475–477

    Article  CAS  PubMed  Google Scholar 

  3. Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 28:10–14

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. Packer NH, von der Lieth C-W, Aoki-Kinoshita KF, Lebrilla CB, Paulson JC, Raman R, Rudd P, Sasisekharan R, Taniguchi N, York WS (2008) Frontiers in glycomics: bioinformatics and biomarkers in disease. An NIH white paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11–13, 2006). Proteomics 8:8–20

    Article  CAS  PubMed  Google Scholar 

  5. Toukach P, Joshi HJ, Ranzinger R, Knirel Y, von der Lieth C-W (2007) Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de. Nucleic Acids Res 35:D280–D286

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  6. Ranzinger R, Frank M, von der Lieth C-W, Herget S (2009) Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences. Glycobiology 19:1563–1567

    Article  CAS  PubMed  Google Scholar 

  7. Ranzinger R, Herget S, Wetter T, von der Lieth C-W (2008) GlycomeDB—integration of open-access carbohydrate structure databases. BMC Bioinformatics 9:384

    Article  PubMed Central  PubMed  Google Scholar 

  8. Herget S, Ranzinger R, Maass K, von der Lieth C-W (2008) GlycoCT—a unifying sequence format for carbohydrates. Carbohydr Res 343:2162–2171

    Article  CAS  PubMed  Google Scholar 

  9. Herget S, Toukach P, Ranzinger R, Hull W, Knirel Y, von der Lieth C-W (2008) Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans. BMC Struct Biol 8:35

    Article  PubMed Central  PubMed  Google Scholar 

  10. Werz DB, Ranzinger R, Herget S, Adibekian A, von der Lieth C-W, Seeberger PH (2007) Exploring the structural diversity of mammalian carbohydrates (“glycospace”) by statistical databank analysis. ACS Chem Biol 2:685–691

    Article  CAS  PubMed  Google Scholar 

  11. Ceroni A, Dell A, Haslam SM (2007) The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures. Source Code Biol Med 2:3

    Article  PubMed Central  PubMed  Google Scholar 

  12. Raman R, Venkataraman M, Ramakrishnan S, Lang W, Raguram S, Sasisekharan R (2006) Advancing glycomics: implementation strategies at the consortium for functional glycomics. Glycobiology 16:82R–90R

    Article  CAS  PubMed  Google Scholar 

  13. Fielding RT (2000) University of California, Irvine Doctoral Dissertation Architectural styles and the design of network-based software architectures University of California, Irvine ©2000 ISBN:0-599-87118-0

    Google Scholar 

  14. Toukach PV (2011) Bacterial carbohydrate structure database 3: principles and realization. J Chem Inf Model 51:159–170

    Article  CAS  PubMed  Google Scholar 

  15. von der Lieth CW, Freire AA, Blank D, Campbell MP, Ceroni A, Damerell DR, Dell A, Dwek RA, Ernst B, Fogh R et al (2011) EUROCarbDB: an open-access platform for glycoinformatics. Glycobiology 21:493–502

    Article  PubMed Central  PubMed  Google Scholar 

  16. Maes E, Bonachera F, Strecker G, Guerardel Y (2009) SOACS index: an easy NMR-based query for glycan retrieval. Carbohydr Res 344:322–330

    Article  CAS  PubMed  Google Scholar 

  17. Lütteke T, Bohne-Lang A, Loss A, Goetz T, Frank M, von der Lieth C-W (2006) GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. Glycobiology 16:71R–81R

    Article  PubMed  Google Scholar 

  18. Cooper CA, Harrison MJ, Webster JM, Wilkins MR, Packer NH (2002) Data standardisation in GlycoSuiteDB. Pac Symp Biocomput 7:297–309

    Google Scholar 

  19. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Cooper CA, Joshi HJ, Harrison MJ, Wilkins MR, Packer NH (2003) GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003 update. Nucleic Acids Res 31:511–513

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  21. Hashimoto K, Goto S, Kawano S, Aoki-Kinoshita KF, Ueda N, Hamajima M, Kawasaki T, Kanehisa M (2006) KEGG as a glycome informatics resource. Glycobiology 16:63R–70R

    Article  CAS  PubMed  Google Scholar 

  22. Bohne-Lang A, Lang E, Förster T, von der Lieth C-W (2001) LINUCS: linear notation for unique description of carbohydrate sequences. Carbohydr Res 336:1–11

    Article  CAS  PubMed  Google Scholar 

  23. McNaught AD (1997) Nomenclature of carbohydrates (recommendations 1996). Adv Carbohydr Chem Biochem 52:43–177

    Article  CAS  PubMed  Google Scholar 

  24. Kikuchi N, Kameyama A, Nakaya S, Ito H, Sato T, Shikanai T, Takahashi Y, Narimatsu H (2005) The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures. Bioinformatics 21:1717–1718

    Article  CAS  PubMed  Google Scholar 

  25. Aoki KF, Yamaguchi A, Ueda N, Akutsu T, Mamitsuka H, Goto S, Kanehisa M (2004) KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res 32:W267–W272

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602-4712, USA

    René Ranzinger & William S. York

Authors
  1. René Ranzinger
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. William S. York
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to René Ranzinger .

Editor information

Editors and Affiliations

  1. Justus-Liebig-University, Giessen, Germany

    Thomas Lütteke

  2. Biognos AB, Göteborg, Sweden

    Martin Frank

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this protocol

Cite this protocol

Ranzinger, R., York, W.S. (2015). GlycomeDB. In: Lütteke, T., Frank, M. (eds) Glycoinformatics. Methods in Molecular Biology, vol 1273. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2343-4_8

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-2343-4_8

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2342-7

  • Online ISBN: 978-1-4939-2343-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation