Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de

Abstract

Functional glycomics, the scientific attempt to identify and assign functions to all glycan molecules synthesized by an organism, is an emerging field of science. In recent years, several databases have been started, all aiming to support deciphering the biological function of carbohydrates. However, diverse encoding and storage schemes are in use amongst these databases, significantly hampering the interchange of data. The mutual online access between the Bacterial Carbohydrate Structure DataBase (BCSDB) and the GLYCOSCIENCES.de portal, as a first reported attempt of a structure-based direct interconnection of two glyco-related databases is described. In this approach, users have to learn only one interface, will always have access to the latest data of both services, and will have the results of both searches presented in a consistent way. The establishment of this connection helped to find shortcomings and inconsistencies in the database design and functionality related to underlying data concepts and structural representations. For the maintenance of the databases, duplication of work can be easily avoided, and will hopefully lead to a better worldwide acceptance of both services within the community of glycoscienists. BCSDB is available at http://www.glyco.ac.ru/bcsdb/ and the GLYCOSCIENCES.de portal at http://www.glycosciences.de/.

Example 1

Retrieval request of references of author ‘Brade’ in year 2002 in any journal. Used was the GLYCOSCIENCES.de advanced bibliographic search (only results are shown). References from BCSDB contain one structure each.

Example 2a

Substructure Search for a-d-Neup5NAc-(2-3)-b-d-Galp in Glycosciences.de using the BCSDB Input wizard.

Example 2b

Result querying GLYCOSCIENCES for all structures containing a specified disaccharide fragment α-d-Neup5Ac-(2→3)β-d-Galp. The data associated with two entries are shown.

Example 3

Querying BCSDB for all structures containing the specified trisaccharide fragment α-d-Galp-(1-3)-α-d-Manp-(1-4)-α-L-Rhap. The GLYCOSCIENCES.de substructure input spreadsheet is used. The data associated with BCSDB entry 10147 are additionally shown.