NOMENCLATURE
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Symbol and Text Nomenclature for Representation of Glycan Structure
The Nomenclature Committee has evaluated widely used symbol nomenclatures and consulted with a variety of interested parties. As a result, the committee selected a version originally put forth by Stuart Kornfeld, later adapted by the editors of the textbook 'Essentials of Glycobiology' (first edition, Cold Spring Harbor Laboratory Press), and further modified it to fit Consortium needs based on the following criteria:
- The symbol nomenclature must be convenient for the annotation of mass spectra. To this end, it was decided that:
- Each sugar type (i.e. sugars of the same mass: hexose, hexosamine and N-acetylhexosamine), should have the same symbol shape.
- Isomers of each sugar type (e.g. mannose/galactose/glucose) should be differentiated by color or by black/white/shading.
- Where possible, the same color or shading should be used for derivatives of hexose (e.g. the corresponding N-acetylhexosamine and hexosamine).
- Representing different sugars using the same shape but different orientation should be avoided so that structures can be represented either horizontally or vertically.
- Colored symbols should still appear distinguishable when copied or printed in black and white.
- Considering 10% of the population is color blind, the use of both red and green for the same shaped symbols should be avoided.
- When desired, linkage information can be represented in text next to a line connecting the symbols (e.g. alpha4, beta4).
Text nomenclature
The Nomenclature Committee recommends a 'modified IUPAC condensed' text nomenclature which includes the anomeric carbon but not the parentheses, and which can be written in either a linear or 2D version. The Committee felt that:
- Including the anomeric carbon is important, and is likely to become increasingly more so in the future as more complicated structures are discovered.
- The presence of parentheses (which then necessitates the use of brackets to indicate branching structures) is unnecessarily cumbersome, particularly when representing the structure in 2D form.
Examples of symbol nomenclature used to illustrate N- and O-linked glycans written in the 2D version of the text nomenclature. Note that symbol structures will be used to annotate data where linkages have not
been defined (e.g MALDI profiling), and if linkages between monosaccharides are known, they can be added above or to the side of the line connecting the symbols if desired (e.g. alpha6 or beta4).
COMING SOON: EXPANDED NOMENCLATURE TO INCLUDE MICROBIAL GLYCANS.
Tool for drawing/annotation of structure can be found at:
http://www.dkfz-heidelberg.de/spec/EUROCarbDB/GlycoWorkbench/
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