EUROCarbDB: An open-access platform for glycoinformatics

Abstract

The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at .

A Brief Review of Bioinformatics Tools for Glycosylation Analysis by Mass Spectrometry

“…7) In this system, MS data can be interpreted by using GlycoWorkbench annotations. According to a theoretical list of fragment masses compared with a list of peaks derived from the spectrum, GlycoWorkbench provides glycan structural constituents based on a collection of fragmentation types.…”

Informatics and Analytical Tools for Glycan Analysis and the Development of Biotherapeutics

“…This was a part of the original EuroCarbDB [52] project, and shares a code-base and basic database structure with both UniCarbKB and UniCarb-DB. However, it has evolved to suit the needs of the chromatography community.…”

“…EuroCarbDB [52] was a European Union (EU)-funded initiative that created the technical framework to support glycobiology research. Even though the project itself is discontinued, the framework lives on as the underlying code in UniCarb-DB [29], UniCarbKB [30], GlycoBase (Dublin) [31], and the continuation of sub-projects, such as GlycanBuilder and GlycoWorkbench [60].…”

Protein Glycosylation and Its Impact on Biotechnology

“…Glycans are composed of monosaccharides and are classified as oligosaccharides (two to 20 monosaccharides) or polysaccharides (more than 20 monosaccharides). The family of monosaccharides consists of 367 different members [8], which are named according to their number of carbon atoms (''triose'' for three carbon atoms or ''hexose'' for six carbon atoms), their functional group (''aldose'' for aldehydes and ''ketose'' for ketone), their ring size (''pyranose'' for a six-membered ring and ''furanose'' for a five-membered ring), and their anomeric carbon atom (orientation of the hydroxyl group on the asymmetric center: D or L, a or b). After incorporation into glycoconjugates, oligosaccharides can be posttranslationally modified by phosphorylation, sulfation, or acetylation.…”