N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
KEYWORDS: CSDB, Carbohydrate Structure Database, Bacterial, Plant, Fungal, Tutorial, Model problems, User manual, Search, Statistics, NMR simulation
chapter in "A Practical Guide to Using Glycomics Databases",
ed.: K.F. Aoki-Kinoshita
Springer Japan, 2017, ch. 5, pp. 75-113, online ISBN 978-4-431-56454-6, print ISBN 978-4-431-56452-2
The main goals of glycoscience are elucidation of carbohydrate features responsible for cellular processes, pathogenicity of microorganisms, and immunological properties of higher organisms, as well as application of glycans as diagnostic and therapeutic agents and classification of natural glycans and glycoconjugates. These goals are hardly achievable without freely available, regularly updated and cross-linked databases, which provide data accumulated in glycoscience and allow tracking of their quality.
The Carbohydrate Structure Database is a curated data repository developed for provision of structural, bibliographic, taxonomic, NMR spectroscopic, and other related information on published carbohydrates and derivatives. Currently it covers ca. 90% of published primary structures of bacterial and archaeal origin and ca. 30% of published primary structures of plant and fungal origin. The data in bacterial part of CSDB are regularly updated. The expansion of plant and fungal coverage is expected in the future. The project aims at coverage close to complete in selected taxonomic domains and at high data quality achieved by manual literature analysis, annotation, verification and data approval. CSDB is freely available on the Internet as a web service at http://csdb.glycoscience.ru.
This chapter presents a step-by-step guide to use CSDB for solving everyday tasks typical for carbohydrate research.