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 http://www.ebi.ac.uk/eurocarb.

Fig. 1.

Carbohydrate representations used in GlycanBuilder. Users can select from five graphical display schemes for glycan structures. As an example structure a complex N-glycan is shown in the IUPAC Text mode, the CFG symbolic format with linkage labels, the CFGL format with linkage positions shown geometrically and the Oxford black & white (UOXF) and color (UFOXCOL) schemes, where linkage positions are shown by geometry and anomeric configurations are denoted by dashed (α) or solid (β) lines. Note that this structure is indefinite since the linkage positions of the terminal GalNAc residues are not defined.

Fig. 2.

Architecture of EUROCarbDB. The core database contains the four components structure, biological context, (experimental) evidence and references. Biological context comprises several categories (blue) which utilize the controlled vocabularies obtained from external databases (NCBI, MeSH). References (green) are also obtained from external databases such as PubMed. A key feature of EUROCarbDB is the internal storage of experimental evidence (right) for a glycan sequence.

Fig. 3.

Proposed experimental workflow for uploading MS data into EUROCarbDB. Starting from acquired raw data, the subsequent use of MS vendor's software (top row) and the newly developed tools Glyco-Peakfinder (middle row) and GlycoWorkbench (bottom row) allows the user to perform structure determination, peak assignments and annotation and data submission to EUROCarbDB.

Fig. 4.

EUROCarbDB web portal. Screenshot demonstrates the information shown for each glycan structure within the database. Features of note include: links to evidence, annotated biological contexts and references, control panel to change graphical representation of structures, automatic superstructure search and main navigation bar.

Fig. 5.

Relationships between analysis tools and the EUROCarbDB. The figure represents the analytical workflows designed for EUROCarbDB, specifically highlighting the central role of the developed tools.