Objectives
Description of DS3-T1
Based on the knowledge accumulated in the partners’ labs and an intensive survey of the literature a report on existing standards and formats HPLC-profiles as well as associated separation procedures 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 and on identifying the already existing data collections and procedures in glycomics research. UOXF.AL will assemble the definitions, conventions, standards for the representation of HPLC profiles and associated separation procedures.
Description of DS3-T2
A comprehensive survey of digital formats, the data flow of experimental data and algorithms for the automatic annotation and storage of HPLC-profiles into databases will be assembled. This compilation will be based on the knowledge accumulated in the partners’ labs as well as on an intensive survey of the literature and the Internet. Eventually, some direct contacts to newly emerging databases and algorithms for the automatic interpretation of HPLC data may be necessary. UOXF.AL will concentrate to evaluate the content of available databases and the reliability, efficiency and transferability of algorithms for HPLC profiles.
Description of DS3-T3
Based on the survey compiled in DS3-T1 and DS3-T2, UOXF.AL and DKFZ will develop concepts and an implementation plan for the automatic flow of HPLC profiles. UOXF.AL and DKFZ will work out the basic concepts and a detailed implementation plan for a reliable, automatic and rapid assignment of HPLC-profiles.
Description of DS3-T4
Based on the knowledge accumulated in the partners’ labs and an intensive survey of the literature, guidelines for quality measures will be formulated, which have to be fulfilled before HPLC profiles can enter the P2P network and subsequently the central database. To guarantee a broad acceptance of the approved quality agreements it will be considered to distribute a questionnaire to other well-known labs for glycan analysis using HPLC techniques, to be sure that all aspects relevant for quality measure have been covered. UOXF.ALwill draft quality measures for the inclusion of for HPLC-profiles. The implementation of the agreed quality measures into the P2P network and the central database will be accomplished by the respective partner and in close co-operation with DS2 partners.
Description of DS3-T5
Based on the survey compiled in DS3-T1 and DS3-T2 and the implementation plan drafted in DS3-T3 DKFZ will implement the algorithms and procedures, which will enable a reliable, automatic and rapid assignment of HPLC profiles. UOXF.AL will provide the corresponding HPLC profiles. UOXF.AL will continuously evaluate the success of the automatic procedures, make suggestion how to improve the underlying algorithms, define experimental data which have to be added to make the procedures more general so that they can be applied to an increasing number of classes of glycans. Additionally, UOXF.AL will appoint the degree of fuzziness for experimental data which can be accepted to cope with varying separation and detection approaches.
Description of DS3-T6
Manuals and tutorials describing the data flow and retrieval options for HPLC profiles will be generated by UOXF.AL. UOXF.AL and DKFZ will provide manuals and tutorials, how to use the implemented procedures for the automatic interpretation of HPLC profiles.
Description of DS3-T7
UOXF.AL will performed an evaluation of the prototype of the P2P network for input, retrieval and interpretation of HPLC spectra. The analysis will be based on the experiences made by the partners in their own labs, a questionnaire which will be sent to selected labs outside the consortium and several internet forums, which will allow interested gylcoscientists to take part in the discussion, report their experiences made using the recommendations made by the consortium. Based on these experiences, recommendations will be formulated describing improvements and new features, which should be included into the fully functional version of the new infrastructure. UOXF.AL will evaluate the reliability of the automatic assignment routines for HPLC-profiles and formulate recommendations for improvements, which should be included into a fully functional new infrastructure to optimise the data flow procedures as well as the reliability of the automatic assignment routines.
EuroCarbDB is a Research Infrastructure Design Study
Funded by the 6th Research Framework Program of the European Union
(Contract: RIDS Contract number 011952)
