EUROCarbDB: An open-access platform for glycoinformatics

Claus-Wilhelm von der Lieth; Ana Arda Freire; Dennis Blank; Matthew P. Campbell; Alessio Ceroni; David R. Damerell; Anne Dell; Raymond A. Dwek; Beat Ernst; Rasmus Fogh; Martin Frank; Hildegard Geyer; Rudolf Geyer; Mathew J. Harrison; Kim Henrick; Stefan Herget; William E. Hull; John Ionides; Hiren J. Joshi; Johannis P. Kamerling; Bas R. Leeflang; Thomas Lutteke; Magnus Lundborg; Kai Maass; Anthony Merry; Rene Ranzinger; Jimmy Rosen; Louise Royle; Pauline M. Rudd; Siegfried Schloissnig; Roland Stenutz; Wim F. Vranken; Goran Widmalm; Stuart M. Haslam

doi:10.1093/glycob/cwq188

EUROCarbDB: An open-access platform for glycoinformatics

Claus-Wilhelm von der Lieth, Ana Arda Freire, Dennis Blank, Matthew P. Campbell, Alessio Ceroni, David R. Damerell, Anne Dell, Raymond A. Dwek, Beat Ernst, Rasmus Fogh, Martin Frank, Hildegard Geyer, Rudolf Geyer, Mathew J. Harrison, Kim Henrick, Stefan Herget, William E. Hull, John Ionides, Hiren J. Joshi, Johannis P. KamerlingBas R. Leeflang, Thomas Lutteke, Magnus Lundborg, Kai Maass, Anthony Merry, Rene Ranzinger, Jimmy Rosen, Louise Royle, Pauline M. Rudd, Siegfried Schloissnig, Roland Stenutz, Wim F. Vranken, Goran Widmalm, Stuart M. Haslam^*

^*Corresponding author for this work

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

Abstract

The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.

Original language	English
Pages (from-to)	493-502
Number of pages	10
Journal	Glycobiology
Volume	21
Issue number	4
DOIs	https://doi.org/10.1093/glycob/cwq188
Publication status	Published - Apr 2011

Funding

The EUROCarbDB initiative (http://www.eurocarbdb.org, Design Studies Related to the Development of Distributed, Web-based European Carbohydrate Databases) was funded by the European Union as a Research Infrastructure Design Study implemented as a Specific Support Action under the FP6 Research Framework Program (RIDS Contract number 011952). D. R. D. is funded by the Biotechnology and Biological Sciences Research Council (BBF0083091 to A. D., S.M.H.).

Keywords

databases
glycoinformatics
informatics tools
open-source
DESORPTION/IONIZATION MASS-SPECTROMETRY
GLYCOPROTEIN GLYCAN STRUCTURES
CURATED RELATIONAL DATABASE
PROTEIN DATA-BANK
CARBOHYDRATE SEQUENCES
GLYCOBIOLOGY RESEARCH
BIOLOGICAL SOURCES
NMR-SPECTROSCOPY
N-GLYCANS
GLYCOSYLATION

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Cite this

von der Lieth, C.-W., Freire, A. A., Blank, D., Campbell, M. P., Ceroni, A., Damerell, D. R., Dell, A., Dwek, R. A., Ernst, B., Fogh, R., Frank, M., Geyer, H., Geyer, R., Harrison, M. J., Henrick, K., Herget, S., Hull, W. E., Ionides, J., Joshi, H. J., ... Haslam, S. M. (2011). EUROCarbDB: An open-access platform for glycoinformatics. Glycobiology, 21(4), 493-502. https://doi.org/10.1093/glycob/cwq188

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title = "EUROCarbDB: An open-access platform for glycoinformatics",

abstract = "The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.",

keywords = "databases, glycoinformatics, informatics tools, open-source, DESORPTION/IONIZATION MASS-SPECTROMETRY, GLYCOPROTEIN GLYCAN STRUCTURES, CURATED RELATIONAL DATABASE, PROTEIN DATA-BANK, CARBOHYDRATE SEQUENCES, GLYCOBIOLOGY RESEARCH, BIOLOGICAL SOURCES, NMR-SPECTROSCOPY, N-GLYCANS, GLYCOSYLATION",

author = "{von der Lieth}, Claus-Wilhelm and Freire, {Ana Arda} and Dennis Blank and Campbell, {Matthew P.} and Alessio Ceroni and Damerell, {David R.} and Anne Dell and Dwek, {Raymond A.} and Beat Ernst and Rasmus Fogh and Martin Frank and Hildegard Geyer and Rudolf Geyer and Harrison, {Mathew J.} and Kim Henrick and Stefan Herget and Hull, {William E.} and John Ionides and Joshi, {Hiren J.} and Kamerling, {Johannis P.} and Leeflang, {Bas R.} and Thomas Lutteke and Magnus Lundborg and Kai Maass and Anthony Merry and Rene Ranzinger and Jimmy Rosen and Louise Royle and Rudd, {Pauline M.} and Siegfried Schloissnig and Roland Stenutz and Vranken, {Wim F.} and Goran Widmalm and Haslam, {Stuart M.}",

year = "2011",

month = apr,

doi = "10.1093/glycob/cwq188",

language = "English",

volume = "21",

pages = "493--502",

journal = "Glycobiology",

issn = "0959-6658",

publisher = "Oxford University Press",

number = "4",

}

von der Lieth, C-W, Freire, AA, Blank, D, Campbell, MP, Ceroni, A, Damerell, DR, Dell, A, Dwek, RA, Ernst, B, Fogh, R, Frank, M, Geyer, H, Geyer, R, Harrison, MJ, Henrick, K, Herget, S, Hull, WE, Ionides, J, Joshi, HJ, Kamerling, JP, Leeflang, BR, Lutteke, T, Lundborg, M, Maass, K, Merry, A, Ranzinger, R, Rosen, J, Royle, L, Rudd, PM, Schloissnig, S, Stenutz, R, Vranken, WF, Widmalm, G & Haslam, SM 2011, 'EUROCarbDB: An open-access platform for glycoinformatics', Glycobiology, vol. 21, no. 4, pp. 493-502. https://doi.org/10.1093/glycob/cwq188

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T1 - EUROCarbDB

T2 - An open-access platform for glycoinformatics

AU - von der Lieth, Claus-Wilhelm

AU - Freire, Ana Arda

AU - Blank, Dennis

AU - Campbell, Matthew P.

AU - Ceroni, Alessio

AU - Damerell, David R.

AU - Dell, Anne

AU - Dwek, Raymond A.

AU - Ernst, Beat

AU - Fogh, Rasmus

AU - Frank, Martin

AU - Geyer, Hildegard

AU - Geyer, Rudolf

AU - Harrison, Mathew J.

AU - Henrick, Kim

AU - Herget, Stefan

AU - Hull, William E.

AU - Ionides, John

AU - Joshi, Hiren J.

AU - Kamerling, Johannis P.

AU - Leeflang, Bas R.

AU - Lutteke, Thomas

AU - Lundborg, Magnus

AU - Maass, Kai

AU - Merry, Anthony

AU - Ranzinger, Rene

AU - Rosen, Jimmy

AU - Royle, Louise

AU - Rudd, Pauline M.

AU - Schloissnig, Siegfried

AU - Stenutz, Roland

AU - Vranken, Wim F.

AU - Widmalm, Goran

AU - Haslam, Stuart M.

PY - 2011/4

Y1 - 2011/4

N2 - The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.

AB - The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.

KW - databases

KW - glycoinformatics

KW - informatics tools

KW - open-source

KW - DESORPTION/IONIZATION MASS-SPECTROMETRY

KW - GLYCOPROTEIN GLYCAN STRUCTURES

KW - CURATED RELATIONAL DATABASE

KW - PROTEIN DATA-BANK

KW - CARBOHYDRATE SEQUENCES

KW - GLYCOBIOLOGY RESEARCH

KW - BIOLOGICAL SOURCES

KW - NMR-SPECTROSCOPY

KW - N-GLYCANS

KW - GLYCOSYLATION

U2 - 10.1093/glycob/cwq188

DO - 10.1093/glycob/cwq188

M3 - Article

SN - 0959-6658

VL - 21

SP - 493

EP - 502

JO - Glycobiology

JF - Glycobiology

IS - 4

ER -

EUROCarbDB: An open-access platform for glycoinformatics

Abstract

Funding

Keywords

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