Toolboxes for a standardised and systematic study of glycans

Matthew P. Campbell; René Ranzinger; Thomas Lütteke; Julien Mariethoz; Catherine A. Hayes; Jingyu Zhang; Yukie Akune; Kiyoko F. Aoki-Kinoshita; David Damerell; Giorgio Carta; Will S. York; Stuart M. Haslam; Hisashi Narimatsu; Pauline M. Rudd; Niclas G. Karlsson; Nicolle H. Packer; Frédérique Lisacek

doi:10.1186/1471-2105-15-S1-S9

Toolboxes for a standardised and systematic study of glycans

Matthew P. Campbell, René Ranzinger, Thomas Lütteke, Julien Mariethoz, Catherine A. Hayes, Jingyu Zhang, Yukie Akune, Kiyoko F. Aoki-Kinoshita, David Damerell, Giorgio Carta, Will S. York, Stuart M. Haslam, Hisashi Narimatsu, Pauline M. Rudd, Niclas G. Karlsson, Nicolle H. Packer, Frédérique Lisacek^*

^*Corresponding author for this work

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Abstract

Background: Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on the structure and function of glycans, their interaction with proteins or their enzymatic synthesis. However, this information is partial, scattered and often difficult to find to for non-glycobiologists. Methods: Following our diagnosis of the causes of the slow development of glycobioinformatics, we review the "objective" difficulties encountered in defining adequate formats for representing complex entities and developing efficient analysis software. Results: Various solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented. Conclusions: Despite the initial stage of our integrative efforts, this paper highlights the rapid expansion of glycomics, the validity of existing resources and the bright future of glycobioinformatics.

Original language	English
Article number	S9
Pages (from-to)	1-11
Number of pages	11
Journal	BMC Bioinformatics
Volume	15
Issue number	S1
DOIs	https://doi.org/10.1186/1471-2105-15-S1-S9
Publication status	Published - 10 Jan 2014

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Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

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Campbell, M. P., Ranzinger, R., Lütteke, T., Mariethoz, J., Hayes, C. A., Zhang, J., Akune, Y., Aoki-Kinoshita, K. F., Damerell, D., Carta, G., York, W. S., Haslam, S. M., Narimatsu, H., Rudd, P. M., Karlsson, N. G., Packer, N. H., & Lisacek, F. (2014). Toolboxes for a standardised and systematic study of glycans. BMC Bioinformatics, 15(S1), 1-11. [S9]. https://doi.org/10.1186/1471-2105-15-S1-S9

Campbell, Matthew P. ; Ranzinger, René ; Lütteke, Thomas ; Mariethoz, Julien ; Hayes, Catherine A. ; Zhang, Jingyu ; Akune, Yukie ; Aoki-Kinoshita, Kiyoko F. ; Damerell, David ; Carta, Giorgio ; York, Will S. ; Haslam, Stuart M. ; Narimatsu, Hisashi ; Rudd, Pauline M. ; Karlsson, Niclas G. ; Packer, Nicolle H. ; Lisacek, Frédérique. / Toolboxes for a standardised and systematic study of glycans. In: BMC Bioinformatics. 2014 ; Vol. 15, No. S1. pp. 1-11.

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title = "Toolboxes for a standardised and systematic study of glycans",

abstract = "Background: Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on the structure and function of glycans, their interaction with proteins or their enzymatic synthesis. However, this information is partial, scattered and often difficult to find to for non-glycobiologists. Methods: Following our diagnosis of the causes of the slow development of glycobioinformatics, we review the {"}objective{"} difficulties encountered in defining adequate formats for representing complex entities and developing efficient analysis software. Results: Various solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented. Conclusions: Despite the initial stage of our integrative efforts, this paper highlights the rapid expansion of glycomics, the validity of existing resources and the bright future of glycobioinformatics.",

author = "Campbell, {Matthew P.} and Ren{\'e} Ranzinger and Thomas L{\"u}tteke and Julien Mariethoz and Hayes, {Catherine A.} and Jingyu Zhang and Yukie Akune and Aoki-Kinoshita, {Kiyoko F.} and David Damerell and Giorgio Carta and York, {Will S.} and Haslam, {Stuart M.} and Hisashi Narimatsu and Rudd, {Pauline M.} and Karlsson, {Niclas G.} and Packer, {Nicolle H.} and Fr{\'e}d{\'e}rique Lisacek",

note = "Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.",

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month = jan,

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Campbell, MP, Ranzinger, R, Lütteke, T, Mariethoz, J, Hayes, CA, Zhang, J, Akune, Y, Aoki-Kinoshita, KF, Damerell, D, Carta, G, York, WS, Haslam, SM, Narimatsu, H, Rudd, PM, Karlsson, NG, Packer, NH & Lisacek, F 2014, 'Toolboxes for a standardised and systematic study of glycans', BMC Bioinformatics, vol. 15, no. S1, S9, pp. 1-11. https://doi.org/10.1186/1471-2105-15-S1-S9

Toolboxes for a standardised and systematic study of glycans. / Campbell, Matthew P.; Ranzinger, René; Lütteke, Thomas; Mariethoz, Julien; Hayes, Catherine A.; Zhang, Jingyu; Akune, Yukie; Aoki-Kinoshita, Kiyoko F.; Damerell, David; Carta, Giorgio; York, Will S.; Haslam, Stuart M.; Narimatsu, Hisashi; Rudd, Pauline M.; Karlsson, Niclas G.; Packer, Nicolle H.; Lisacek, Frédérique.

In: BMC Bioinformatics, Vol. 15, No. S1, S9, 10.01.2014, p. 1-11.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Toolboxes for a standardised and systematic study of glycans

AU - Campbell, Matthew P.

AU - Ranzinger, René

AU - Lütteke, Thomas

AU - Mariethoz, Julien

AU - Hayes, Catherine A.

AU - Zhang, Jingyu

AU - Akune, Yukie

AU - Aoki-Kinoshita, Kiyoko F.

AU - Damerell, David

AU - Carta, Giorgio

AU - York, Will S.

AU - Haslam, Stuart M.

AU - Narimatsu, Hisashi

AU - Rudd, Pauline M.

AU - Karlsson, Niclas G.

AU - Packer, Nicolle H.

AU - Lisacek, Frédérique

N1 - Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

PY - 2014/1/10

Y1 - 2014/1/10

N2 - Background: Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on the structure and function of glycans, their interaction with proteins or their enzymatic synthesis. However, this information is partial, scattered and often difficult to find to for non-glycobiologists. Methods: Following our diagnosis of the causes of the slow development of glycobioinformatics, we review the "objective" difficulties encountered in defining adequate formats for representing complex entities and developing efficient analysis software. Results: Various solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented. Conclusions: Despite the initial stage of our integrative efforts, this paper highlights the rapid expansion of glycomics, the validity of existing resources and the bright future of glycobioinformatics.

AB - Background: Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on the structure and function of glycans, their interaction with proteins or their enzymatic synthesis. However, this information is partial, scattered and often difficult to find to for non-glycobiologists. Methods: Following our diagnosis of the causes of the slow development of glycobioinformatics, we review the "objective" difficulties encountered in defining adequate formats for representing complex entities and developing efficient analysis software. Results: Various solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented. Conclusions: Despite the initial stage of our integrative efforts, this paper highlights the rapid expansion of glycomics, the validity of existing resources and the bright future of glycobioinformatics.

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U2 - 10.1186/1471-2105-15-S1-S9

DO - 10.1186/1471-2105-15-S1-S9

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C2 - 24564482

AN - SCOPUS:84901273059

VL - 15

SP - 1

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JO - BMC Bioinformatics

JF - BMC Bioinformatics

SN - 1471-2105

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ER -

Toolboxes for a standardised and systematic study of glycans

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