Although the two-dimensional notation of glycans as in figure below may be visually appealing, it is not suitable for storage in a database, and bioinformatic analysis tools would not be able to make use of it. Thus the IUPAC-IUBMB (International Union of Pure and Applied Chemistry - International Union of Biochemistry and Molecular Biology) has specified the "Nomenclature of Carbohydrates" to uniquely describe complex oligosaccharides based on a three-letter code to represent monosaccharides.

For example, gal represents galactose and man represents mannose; a listing of the common monosaccharides (and their derivatives) that occur in oligo- and polysaccharides is given in Table below (Tsai (2007)). Each monosaccharide code is preceded by the anomeric descriptor and the configuration symbol. The ring size is indicated by an italic f for furanose or p for pyranose. The carbon numbers that link the two monosaccharide units are given in parentheses between the symbols separated by an arrow. Double-headed arrows may be used if monosaccharides are linked through their anomeric centers. Moreover, α and β may be represented as a or b, respectively. In such a way, long carbohydrate sequences can be adequately described in abbreviated form using a sequence of letters.

α-D-Manp-(1→3)[α-D-Manp-(1→6)]-β-D-Manp-(1→4)-β-D-GlcpNAc-(1→4)-β-D-GlcpNAc-(1→

Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-

Linear Code® is a carbohydrate format that uses a single-letter nomenclature for monosaccharides and includes a condensed description of the glycosidic linkages. Monosaccharide representation is based on the common structure of a monosaccharide where modifications to the common structure are indicated by specific symbols, as in the following (Banin et al. (2002)).

• Stereoisomers (D or L) differing from the common isomer are indicated by apostrophe (’).
• Monosaccharides with differing ring size (furanose or pyranose) from the common form are indicated by a caret (^).
• Monosaccharides differing in both of the above are indicated by a tilde (˜).

Ma3(Ma6)Mb4GNb4GN

The KEGG Chemical Function (KCF) format for representing glycan structures was originally used to represent chemical structures (thus the name) in KEGG. KCF uses the graph notation, where nodes are monosaccharides and edges are glycosidic linkages. Thus to represent a glycan, at least three sections are required: ENTRY, NODE, EDGE, followed by three slashes ‘///’ at the end.

• The ENTRY section consists of one line and may specify a name for the structure followed by the keyword Glycan.
• The NODE section consists of several lines. The first line contains the number of monosaccharides or aglycon entities, and the following lines consist of the details of these entities numbered consecutively. For each entity line, the name and x- and y-coordinates (to draw on a 2D plane) must be specified.
• Similarly, the EDGE section consists of several lines, the first line containing the number of bonds (usually one less than the number of NODEs), followed by the details of the bond information. The format for the bond information is as follows:
  
  num     <donor node#>:<anomeric configuration (a or b)><donor carbon#>     <acceptor node#>:<acceptor carbon#>

ENTRY     XYZ          Glycan
NODE      5
          1     GlcNAc     15.0     7.0
          2     GlcNAc      8.0     7.0
          3     Man         1.0     7.0
          4     Man        -6.0    12.0
          5     Man        -6.0     2.0
EDGE      4
          1     2:b1       1:4
          2     3:b1       2:4
          3     5:a1       3:3
          4     4:a1       3:6
///
          

Web3 Unique Representation of Carbohydrate Structures (WURCS) as a linear notation for representing carbohydrates for the Semantic Web.

WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1