Objectives
Description of DS2-T1
DKFZ and EMBL-EBI will compile - mainly based intensive literature search and browsing the Internet - a comprehensive overview of existing P2P networks, the areas for which such networks are in use, the purposes they are used for, the existing technical implementations, their functionality and the experiences, which are made with their use in practice. Based on this overview, DKFZ and EMBL-EBI will develop the basic concepts for a P2P network and the corresponding central database, which fits best with the needs of glycobiology / glycomics projects. Based on this preparatory work DKFZ and EMBL-EBI will develop a detailed implementation plan for the P2P network as well as the central database and the storage facility. Since the technical design of the P2P network exhibits mainly a challenge in informatics, only moderate subject specific input from the other design studies is required for this sub-task. However, the concept should be so flexible that it can be easily adopted to subject specific need.
Description of DS2-T2
Based on the worked out concept, DKFZ and EMBL-EBI will develop a first draft of the P2P network, install the corresponding databases at both institutions and test and improve subsequently the communication between both independent clients of the network, try out and advance the dependability of the network and optimise the design of the database to enhance the access speed. When a good steadiness has been reached, BCU will be included into the network. The reliability of the procedures to install the network and the underlying databases on computers of external partners will be evaluated and improved. Subsequently all parts of the P2P network will be optimised, so that one additional partner of the consortium can be added to evaluate the functionality of the network. Based on implementation of the P2P network EMBL-EBI will evaluate the concept for central database and the storage facility and arrange the required technical requirements.
Description of DS2-T3
Based on the specifications made by DS1 concerning the general description to characterize glycan structures, their occurrence in nature and their biological functions and based on the commitments for the description of MS- and NMR data made by DS3 and DS4, DKFZ and EMBL-EBI will adapt the database-design, the input facilities as well as retrieval options and the digital export format, so that all functions fit optimal with the needs of glycobiology research as well as glycomics projects. DKFZ will include the MS and HPLC modules developed by DS3. BCU will concentrate to implement the NMR modules developed in close cooperation with DS4. EMBL-EBI will establish the central database and the associated storage facility. By degree a first fully functional version of the prototype of the P2P network will be made available for all partners of the consortium. The partners will try out the input and retrieval options and make suggestions how to optimise the procedures for the specific needs of the various experimental techniques.
Description of DS2-T4
A central aim of the emerging glycomics projects is to create a cell-by-cell catalogue of glycosyltransferase expression and detected glycan structures. EMBL-EBI - in close cooperation with the subcontractor - will develop concepts and implement strategies for automatic cross-linking/ with genomics and proteomics databases. A comprehensive survey of available databases containing glyco-related data, their scientific impact for this consortium and the digital formats the data are available will be compiled. Based on the suggestion made by the subcontractor, a first draft of a cell-by-cell catalogue of glycan structures and glycosyltransferases will be created. On the basis of a limited amount of data included by the subcontractor, EMBL-EBI will compile a survey of the thinkable strategies how the glyco-relevant data can be automatically cross-referenced and linked with existing genomics and proteomics data. In addition, EMBL-EBI will perform an analysis how to connect glyco-related of information available in distributed databases and so far unstructured flat files into the P2P network.
Description of DS2-T5
A detailed description of all parts of the network, how to connect, how to use it and how to input new data is a crucial factor for wide acceptance of a new infrastructure. The manuals and tutorials for user input and retrieval options, which will be prepared mainly to guide and help the partners of the consortium, will be elaborated in such a way that they can be easily adopted for a broader range of users. EMBL-EBI will be responsible for the description of the hard- and software requirement, how to install the databases and how to connect to the network. Additionally, EMBL-EBI will provide a detailed description of the database design. DKFZ and BCU will prepare manuals and tutorials how to include and retrieve experimental data. DKFZ will concentrate on MS and HPLC related data, BCU will focus on NMR related data.
Description of DS2-T6
DKFZ, BCU as well as EMBL-EBI will implement the advanced tools for automatic interpretation of MS, HPLC and NMR spectra developed by DS3 and DS4. Whereas DKFZ will concentrate to include the MS and HPLC related procedures, BCU will focus on the corresponding procedures for NMR spectroscopy. EMBL-EBI will be responsible for the integration of agreements made by DS1 and overlook general aspects of the implementation of components into the P2P network, so that all modules work smoothly together using the same interface. EMBL-EBI will implement the linking and cross-referencing strategy with other databases as far as developed under DS2-T4.
EuroCarbDB is a Research Infrastructure Design Study
Funded by the 6th Research Framework Program of the European Union
(Contract: RIDS Contract number 011952)
