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Toolboxes for a standardised and systematic study of glycans.

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 - BMC Bioinformatics (2014)

Bottom Line: However, this information is partial, scattered and often difficult to find to for non-glycobiologists.Various solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented.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.

View Article: PubMed Central - HTML - PubMed

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.

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Graphical representation of glycans. Examples for graphical representations of glycan structures corresponding to the illustration of Figure 1. (A) CFG cartoon representation using colour symbols. (B) CFG cartoon representation using greyscale symbols. (C) Oxford cartoon representation. (D) IUPAC like representation using textual names. (E) Chemical representation preferred by carbohydrate chemists. A definition of the symbols and corresponding monosaccharide names is shown below (E).
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Figure 2: Graphical representation of glycans. Examples for graphical representations of glycan structures corresponding to the illustration of Figure 1. (A) CFG cartoon representation using colour symbols. (B) CFG cartoon representation using greyscale symbols. (C) Oxford cartoon representation. (D) IUPAC like representation using textual names. (E) Chemical representation preferred by carbohydrate chemists. A definition of the symbols and corresponding monosaccharide names is shown below (E).

Mentions: Admittedly, formats shown in Figure 1 are manifestly machine-readable but do not really meet user-friendliness standards. Consequently, in addition to the sequence encoding of structures, several graphical representations are supported by a majority of glyco-focused databases. Figure 2 shows several graphical representations of the glycan described in Figure 1. Here, the monosaccharide names are replaced by symbolic representations, so called cartoons (Figure 2A-C), or by depictions of the chemical structure (Figure 2E). Examples of cartoons are the representation scheme developed by the "Essentials in Glycobiology" textbook editors (and adopted by the CFG) (Figure 2A, B) [2] and the scheme developed by the Oxford Glycobiology Institute [23,24] (Figure 2C). A combination of both these formats in which the linkages are depicted as angles as in the Oxford scheme on the residue symbols of the 'Essentials in Glycobiology' scheme can also be found in web interfaces (such as UniCarbKB) and publications (not shown in Figure 2). In many scientific articles graphics following the monosaccharide names and linkages as defined by the IUPAC nomenclature (Figure 2D) are used. The chemical representation of the glycan (Figure 2E) is preferred by groups that work on the synthesis of glycan structures or on glycan analysis by NMR. EUROCarbDB, GlycomeDB and UniCarbKB [25] have implemented user-interface features that enable switching between supported graphical formats. This feature is made possible by integrating GlycanBuilder [26,27], a tool developed in partnership with EUROCarbDB, which produces graphical representations of glycan structures (see below for more details).


Toolboxes for a standardised and systematic study of glycans.

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 - BMC Bioinformatics (2014)

Graphical representation of glycans. Examples for graphical representations of glycan structures corresponding to the illustration of Figure 1. (A) CFG cartoon representation using colour symbols. (B) CFG cartoon representation using greyscale symbols. (C) Oxford cartoon representation. (D) IUPAC like representation using textual names. (E) Chemical representation preferred by carbohydrate chemists. A definition of the symbols and corresponding monosaccharide names is shown below (E).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4016020&req=5

Figure 2: Graphical representation of glycans. Examples for graphical representations of glycan structures corresponding to the illustration of Figure 1. (A) CFG cartoon representation using colour symbols. (B) CFG cartoon representation using greyscale symbols. (C) Oxford cartoon representation. (D) IUPAC like representation using textual names. (E) Chemical representation preferred by carbohydrate chemists. A definition of the symbols and corresponding monosaccharide names is shown below (E).
Mentions: Admittedly, formats shown in Figure 1 are manifestly machine-readable but do not really meet user-friendliness standards. Consequently, in addition to the sequence encoding of structures, several graphical representations are supported by a majority of glyco-focused databases. Figure 2 shows several graphical representations of the glycan described in Figure 1. Here, the monosaccharide names are replaced by symbolic representations, so called cartoons (Figure 2A-C), or by depictions of the chemical structure (Figure 2E). Examples of cartoons are the representation scheme developed by the "Essentials in Glycobiology" textbook editors (and adopted by the CFG) (Figure 2A, B) [2] and the scheme developed by the Oxford Glycobiology Institute [23,24] (Figure 2C). A combination of both these formats in which the linkages are depicted as angles as in the Oxford scheme on the residue symbols of the 'Essentials in Glycobiology' scheme can also be found in web interfaces (such as UniCarbKB) and publications (not shown in Figure 2). In many scientific articles graphics following the monosaccharide names and linkages as defined by the IUPAC nomenclature (Figure 2D) are used. The chemical representation of the glycan (Figure 2E) is preferred by groups that work on the synthesis of glycan structures or on glycan analysis by NMR. EUROCarbDB, GlycomeDB and UniCarbKB [25] have implemented user-interface features that enable switching between supported graphical formats. This feature is made possible by integrating GlycanBuilder [26,27], a tool developed in partnership with EUROCarbDB, which produces graphical representations of glycan structures (see below for more details).

Bottom Line: However, this information is partial, scattered and often difficult to find to for non-glycobiologists.Various solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented.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.

View Article: PubMed Central - HTML - PubMed

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.

Show MeSH
Related in: MedlinePlus