Chapter 10 - Carbohydrate Structure Databases

Abstract

The availability of databases and tools to store, retrieve, and analyze data in an efficient way is of fundamental importance to progress in glycomics. This chapter describes major, well-established databases and introduces two new database initiatives. Each database uses a particular sequence format to encode carbohydrate structures. Therefore, there is hardly any cross-linking between the established databases. There are nine major database projects dedicated to the storage of carbohydrate structures: seven of these follow an open access policy, while two more are commercial and thus follow a more restricted access model. The open access databases have different capabilities to perform queries. Most of the projects offer structural searches to some extent, while the additional query functions are highly diverse, indicating a specialization of the individual databases. Future database initiatives are undertaken owing to the lack of a comprehensive database for storage and retrieval of carbohydrate structures in glycomics and glycobiology research. EUROCarbDB project aims to support the analytical process of carbohydrate structure determination from the spectrometer to database storage. Its fundamental ethics involve freely accessible data and open source tools. GlycomeDB is another initiative involving the translation of freely available databases to the GlycoCT sequence format. This format is stored in a new database to overcome the isolation of the carbohydrate structure databases and to create a comprehensive index of all available structures with references back to the original databases. Two case studies demonstrating how existing database resources can be used to answer specific scientific questions are analyzed.