Objectives
Current status
The development of informatics for glycobiology is a very young field of research. Until recently only very few databases were available. The current growth of new databases and applications is mainly driven by the need to create algorithms for automatic interpretation of experimental data produced by the upcoming glycomics projects. However, most projects are designed to support specific scientific questions and do not intend to share data with other applications. The reported internal data formats vary considerably. DS1-T1 and DS1-T2 will compile a comprehensive overview of existing experimental approaches whereas DS1-SUB1 will compile a survey of the structural complexity of carbohydrates and their profiles of occurrence in various tissues, species and cells. The exchange of data, their cross-linking and referencing between various projects is seriously hampered by the lack of generally accepted digital exchange formats, standardized structural and biological descriptions. To surmount this unfavourable situation DS1-T3 will formulate recommendations for the encoding of glycan structures as well as the documentation of experiments in glycomics projects. Another obstacle are missing quality measures for experimental data, which have to be fulfil before new data will be included into the database. DS1-T3 aims to overcome this problem for the structural description of glycans whereas DS1-SUB3 will provide recommendations how to encode biological data. There are only a few attempts to overcome the lack of appropriate structural description for complex carbohydrates by the US consortium of Functional Glycomics as well as the IUPAC/IUBMB committee for carbohydrate nomenclature. DS1-T5 will provide a central depository for carbohydrate registry numbers, which will enable an efficient cross-link of existing and newly emerging databases in the realm of glycobiology.
The Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification. Like in glycomics research, widely accepted public repositories for mass spectrometry based protein identifications do not exist; detailed experimental results are usually not available. A standard way to represent proteomics as well as glycomics data, and an agreed minimum required level of detail, are both urgently required to facilitate the analysis, dissemination and exchange of proteomics and glycomics data. The PSI Mass Spectrometry work group develops a standard representation of experimental spectra in the context of the experimental setup and the analysed system. The extra requirements for glycomics specifications in import/export for analytical techniques, observations and cross-referencing will be analysed in DS1-T1 and DS1-T2 and the recommendation made in DS1-T3 should fit into existing proteomics schemes
EuroCarbDB is a Research Infrastructure Design Study
Funded by the 6th Research Framework Program of the European Union
(Contract: RIDS Contract number 011952)
