Objectives
Description of DS4-T1
Based on the knowledge accumulated in the partners’ labs and an intensive survey of the literature a report on the availability of existing NMR-standards and public available databases containing NMR to detect glycans will be compiled. The survey will focus on the scientific importance of the experimental data with respect to ongoing glycomics projects, the technical requirements to enable an automatic inclusion of experimental data into a database structure and on identifying the already existing data collections and procedures in glycomics research. BCU will focus to survey the experimental techniques used, SU will concentrate on existing data collection and their potential use for the consortium and UBA will elaborate on described procedures for automatic assignment of glycans using various NMR techniques.
Description of DS4-T2
Based on the comprehensive survey compiled in DS4-T1, BCU, SU and UBA will formulate guidelines for a uniform representation of NMR data, which shall be entered into the database. These guidelines include also rules of a user-friendly web-interface, which allows entering structural and spectroscopic data in a way, which reflects the common practice of NMR experimentalists. The availability of well-approved procedures will be of central prominence for the wide acceptance of the input procedure and thus the whole design study. BCU and UBA will focus on guidelines for a uniform representation, whereas SU will concentrate on the formulation of guidelines for the input procedures. The partners of DS2 include the commitments made by the DS4 partners into the P2P network of databases.
Description of DS4-T3
Based on the knowledge accumulated in the partners’ labs and an intensive survey of the literature, guidelines for agreements about quality measures of NMR spectra will be formulated. These directives have to be fulfilled before an NMR spectrum will included into the database. Additionally, recommendations for protocols how to prepare glycan probes and the type of NMR procedures, which shall be preferably applied to ensure a defined level of quality of data which enter the database, will be drafted. All three partners will equally contribute to the formulation of these recommendations.
Description of DS4-T4
SU and UBA will work on algorithms for automatic interpretation of NMR-spectra. SU will concentrate to enhance the rule based interpretation system developed at Stockholm University, which is until now restricted to the interpretation of NMR-spectra from bacterial polysaccharides. The aim is to expand the existing set of rules in such a way, so that also the NMR spectra of other classes of glycans can be estimated. UBA will focus to enhance the automatic interpretation of NMR spectra using Artificial Neural Networks (ANNs). The University of Basel has recently made available a preliminary version of an ANN approach for the analysis of 13C-NMR data of mammalian oligosaccharides. The aim of this task is to train the ANNs for additional classes of glycans, so that a classifications scheme results, which is applicable for an increasing number of glycan structures.
Description of DS4-T5
BCU will generate manuals and tutorials describing the user input and retrieval options for NMR spectra. SU will provide a manual and tutorials, how to use the increment rules for an automatic interpretation of NMR spectra. UBA will provide a manual and tutorials, how to use the ANN approach for an automatic interpretation of NMR spectra.
Description of DS4-T6
All three partners of the subtask will perform the evaluation of the prototype of the P2P network for input, retrieval and interpretation of NMR spectra. The analysis will be based on the experiences made by the partners in their own labs, a questionnaire will be sent to selected labs outside the consortium and internet forums, which will allow interested glycoscientists to take part in the discussion and report their experiences made using the recommendations made by the consortium. Based on these experiences, recommendations will be formulated for improvements and new features, which should be included into the fully functional version of the new infrastructure. Suggestions will be elaborated, which classes of complex carbohydrates and experimental approaches for NMR should be included into a fully functional new infrastructure. Additionally, it will be an important task to compare predictive power of various approaches dedicated for the automatic interpretation of NMR-spectra of complex carbohydrates.
EuroCarbDB is a Research Infrastructure Design Study
Funded by the 6th Research Framework Program of the European Union
(Contract: RIDS Contract number 011952)
