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Design Studies related to the development of distributed, Web-based European Carbohydrate Data Bases

Final Report Summary - EUROCarbDB (Design Studies related to the development of distributed, Web-based European Carbohydrate Data Bases)

The 'Design Studies Related to the Development of Distributed, Web-based European Carbohydrate Databases' (EUROCarbDB) design study was initiated to develop a new infrastructure which will constitute the nucleus for a central depository for carbohydrate-related data (structure and function), comparable to and cross-linked with the extensively used genomics and proteomics data collections.

The technical framework shall be established for a bottom-to-top initiative where all interested research groups can input their primary data and interpreted results. The initiative aims to provide systematically integrated tools for streamlining European research in glycobiology through the development of databases, bioinformatics standards, efficient analysis and search algorithms, and web-based software components.

To maximise synergism, other available bioinformatics and biomedical resources will be linked to the newly created databases and cross-referenced in an efficient way. One major aim of the EUROCarbDB design study is the development of appropriate algorithms and tools which facilitate the rapid and reliable processing, interpretation and annotation of analytical data for glycan structure determination with a high degree of automation. This effort for the glycomics field is comparable to the development of the highly automated techniques for nucleic acid sequencing which have so successfully accelerated genomics studies and enabled their large scale application.

The EUROCarbDB project is expected to provide comparable impetus in glycomics. The EUROCarbDB study has concentrated on the evaluation and development of the basic requirements for the proposed infrastructure.

The design goals and concepts of EUROCarbDB are far-reaching and by no means limited to the time frame or extent of the current project. The architecture of the database has been conceived to allow at a later stage further types of experimental data to be added, e.g. three-dimensional structures derived from X-ray studies, protein-carbohydrate binding studies, multidimensional nuclear magnetic resonance (NMR) spectra, carbohydrate microarrays, microcalorimetry, surface plasmon resonance, or collections of methods for chemical, combinatorial, chemo-enzymatic and large-scale synthesis of glyco-probes.

Above all, EUROCarbDB has been conceived as an open-access, open-source project devoted entirely to the use of web-based or downloadable free software, whereby the users are encouraged to contribute not only data and error reports but also ideas for improvements and extensions.