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CSDB Linear
IUPAC Condensed
LINUCS
WURCS
CSDB Linear is the rules for encoding of carbohydrate and derivative structures in a single line.
You may need this information in three cases:
- if you plan to use the expert form of query when searching for a substructure
- if you are going to submit your data to CSDB
- if you are establishing an automated cross-database data exchange
Example of CSDB Linear format: The N-glycan core structure represented in CSDB Linear format.
P-7)aXDDmanHepp(1-P
This format is the most commonly used in various publications, databases and web pages as a rather compact but yet human-readable representation of carbohydrates.
Example of IUPAC Condensed format: The N-glycan core structure represented in IUPAC Condensed format.
Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)b-GlcNAc
LINUCS is LInear Notation for Unique description of Carbohydrate Sequences.
LINUCS was chosen to fulfil to following conditions:
- input of extended, non-graphic nomenclature to describe carbohydrate structures
- resulting linear code is closely related to notations and abbreviations
- recommended by IUPAC
- number of additional rules to define the priority of the branches is low
- extended nomenclature of complex carbohydrates contains all information to define the hierarchy
- LINUCS is applicable to all types of carbohydrates (macrocyclic system are currently not implemented)
- remaining unassigned linkage information are tolerated
Example of LINUCS format: The N-glycan core structure represented in LINUCS format.
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}
Web3 Unique Representation of Carbohydrate Structures (WURCS) as a linear notation for representing carbohydrates for the Semantic Web.
Example of WURCS format: The N-glycan core structure represented in WURCS format.
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