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Symbol nomenclature for representing glycan structures: Extension to cover different carbohydrate types
Author(s) -
Harvey David J.,
Merry Anthony H.,
Royle Louise,
Campbell Matthew P.,
Rudd Pauline M.
Publication year - 2011
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201100300
Subject(s) - monosaccharide , glycobiology , symbol (formal) , pyranose , computer science , variety (cybernetics) , set (abstract data type) , extension (predicate logic) , nomenclature , artificial intelligence , computational biology , glycan , chemistry , biology , stereochemistry , biochemistry , programming language , ecology , taxonomy (biology) , glycoprotein
This Viewpoint article addresses comments made on our original article describing a symbolic system for the depiction of N ‐ and O ‐linked carbohydrate structures and proposes a method for extending the symbol set to include monosaccharides commonly found in carbohydrates present in bacteria and plants. As before, basic monosaccharides are shown by shape with one or more additions such as solid fill or additions of lines, crosses or dots to represent functional groups. The use of colour to differentiate constituent monosaccharides is avoided, thus enabling the system to be used in a variety of formats. Linkage and anomericity are shown by the angle and type of line connecting the symbols. In this extended version, new symbols are proposed for additional hexoses and it is proposed that pyranose and furanose forms of the monosaccharides could be shown by solid or broken outlines to the symbols. Conventions for depicting the presence of multiple functional groups such as deoxy‐(NH 2 ) 2 are also discussed. It is hoped that these proposals will stimulate discussion so that a consensus can be reached as to how the glycobiology community can best convey complex information in a simple manner.