Objectives
Current status
The current situation in glycobiology can be characterized by a nearly complete loss of all primary experimental data. Most of these data are either not published (MS-spectra, HPLC-profiles, often NMR spectra) or are distributed in various journals using different notations, assignments and data formats. In contrast to the genomic and proteomic area, no generally accepted open access depository for glyco-related experimental data exists at present. The idea to establish for a peer-to-peer network of distributed scientific databases is new and has so far not been implemented and tested to relocate the error-prone and expensive task of keeping a database up to date to the scientists who are recording the primary data.
Currently, glyco-related databases and bioinformatics tools are not intensively used to investigate scientific questions in the realm of glycobiology. One of the obvious reasons for this underdevelopment compared to the proteomics and genomics area is that no intensive cross-referencing between the glycan containing databases and proteomics and genomics data exist. DS2-T4 together with the subcontract tries to analyse the basic requirement to overcome this unfavourable situation. DS2-SUB2 will provide recommendations for a digital cell-by-cell catalogue of glycan structures and glycosyltransferases. DS2-SUB4 focuses on advanced cross-linking strategies to establish relationships between glycosylation and its biomedical importance.
DS2-T1, DS2-T2 and DS2-T3 aim to establish the foundation for a prototype of a P2P network of databases, which will enable research groups to manage, assign and deposit the experimental data, which have been recorded in their labs. Furthermore, the willingness to deposit experimental data is hampered by the lack of generally accepted digital exchange formats, standardized structural and biological descriptions as well as missing quality measures for experimental data. DS1 (for general descriptions of glycans), DS3 (for MS and HPLC data) and DS4 (for NMR data) will develop these standards, which will subsequently be implemented into the prototype of the P2P network of virtually connected databases.
EuroCarbDB is a Research Infrastructure Design Study
Funded by the 6th Research Framework Program of the European Union
(Contract: RIDS Contract number 011952)
