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Primary structure of Carbohydrates and their biological occurence

Objectives


Description of DS1-T1

Based on the experiences made by the partners in their own labs and an intensive survey of the literature a report on experimental techniques to detect glycans, which are currently used in glycomics / glycobiology research, will be compiled. ICL and UGI will focus on summarizing the current status in mass spectrometry and the related separation methods.  UOXF.AL will address HPLC based separation and identification, whereas BCU, SU and UBA will concentrate on the development in NMR spectroscopy. 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. Part of the task will be to evaluate the suitability for glycobiology in adopting one of the existing concerted efforts in creating interchange standards for technique and proteomics data.

Description of DS1-T2

Currently, different ways to describe and encode carbohydrate structures are in use in glycomics / glycobiology projects and are reported in the literature. Since the structural descriptions of glycans will be the most important way to access the stored data, a comprehensive overview of the currently used digital descriptions used the literature and the participating labs will be compiled. All partners will be involved in the compilation and discussion of the structural description of glycans, since this notation is fundamental to all scientific braches of glycosciences. DKFZ and EMBL-EBI will focus on how efficiently the available digital descriptions can be used in databank applications. The other partners will have to evaluate, if proposed structural descriptions allow to encode all types of glycans in various organisms, how close the representation fits with existing nomenclatures (BCU, SU, ICL and UGI) how many rules are required to build up a unique hierarchy. Another mission will be to find out how flexible a digital description has to be designed to cope with inherent structural variability at the non reducing ends of glycans to tolerate some fuzziness in the structural description of complex glycans (DKFZ, EMBL-EBI in close co-operation mainly with ICL, UOXF.AL and UGI and the other partners).

Description of DS1-T3

The results of the details analysis made in DS1-T1 and DS1-T2 will form the basis for recommendations for the encoding and representation of glycan structures as well as the documentation of experiments in glycomics and proteomics projects. To ensure a broad acceptance within the glycosciences-community, expert opinions will be called in, Internet forums to discuss the recommendations will be established and whenever appropriate, widely accepted and often used descriptions should be taken over. Predefinitions made by other consortia (US-CFG, HUPO-HGPI, GLYCOSCIENCES.de) should be preferentially considered and only declined in case there are substantial objections against a certain definition or format. In particular the existing concerted efforts in creating interchange standards for technique and proteomics data have to evaluate for the suitability for glycobiology. The same is true for definitions that include Nuclear Magnetic Resonance spectroscopy and Mass Spectrometry. ICL and UGI will focus on drafting the recommendations in mass spectrometry and the related separation methods. UOXF.AL will concentrate on HPLC based separation and identification techniques, whereas BCU, SU and UBA will address the recommendations in NMR spectroscopy. All partners will be engaged preparing the guidelines for the structural description.

Description of DS1-T4

The reproducibility of recorded data in various laboratories is a fundamental requirement for information, which shall be included into a well-organised database. Since varying procedures to purify and separate glycans from others constituent parts of biological material to be analysed exist, an evaluation of commonly used protocols in different labs will be performed. The evaluation will be based on the experiences made by the partners in their own labs, an intensive survey of the literature and a questionnaire, which will be sent to selected labs outside the consortium. Additionally, the questionnaire will be made available through the Internet. ICL and UGI will focus on in mass spectrometry and the related separation methods.  UOXF.AL will address HPLC based separation and identification techniques, whereas BCU, SU and UBA will concentrate on procedures in NMR spectroscopy. To evaluate, how much the reproducibility of the recorded data depends on the preparative techniques used to purify and separate glycans, the same probes will be analysed using various preparation methods and analytical techniques. These tests will result in the formulation guidelines describing the data, which should preferably enter into database.

Description of DS1-T5

It is well know from genomics, proteomics as well as chemometrics, that the creation of a unique key to describe a certain molecule is the most efficient way to unambiguously identify a certain compound and to link various databases. Based on the structural description to encode glycan structures as defined in task DS1-T3, DKFZ, and EMBL-EBI will develop algorithms and procedures, which generate a unique key for each glycan structure. These procedures will require the topology of the glycan structure as often used publications as sole input. A central repository for carbohydrate registry numbers will be made publicly available at DKFZ as well as at EMBL-EBI. Everybody through the Internet can automatically access the registry number. An internet forum will enable and intensive exchange of experiences made by external users using the glycan registry tool. In such a way, the information associated with a given glycan structure can be unambiguously linked between various databases In addition, the classification of the glycan (N-,O-glycan having a certain number of antenna) will be provided as well as a list of known biological occurrence of the requested glycan.

Description of DS1-T6

The main purpose of this task will be to evaluate the practicability and usability of the definitions, recommendations and guidelines developed under task DS1-T1 to DS1-T5. Based on the experiences made, suggestions for a revised version will be prepared. DKFZ, EMBL-EBI and SU will have to evaluate if the digital encoding schemes are conform with the requirements of glycobiology research in general and the needs of glycomics projects in particular. ICL and UGI will focus to evaluate the practicability of the made recommendation for mass spectrometry and the related separation methods: UOXF.AL will work on HPLC based separation techniques, whereas BCU, SU and UBA will elaborate on procedures for NMR spectroscopy. The evaluation 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 all interested glycoscientists to take part in the discussion, report their experiences made using the recommendations and make suggestions to improve the descriptions and guidelines. Extensions of recommendations will be included in areas of glycobiology, which are difficult to handle and have therefore not been included at the beginning of the project, but should be contained in a fully developed new infrastructure. Especially recommendations for the structural descriptions of non-stoichiometric substitutions as present in protein glycans and glycosaminoglycans as well as rarely occurring monosaccharides and unusual linkages will be required.

Description of DS1-SUB1

Based on his own experiences and an intensive survey of the literature the subcontractor will compile a comprehensive survey of structural complexity of carbohydrates and their profiles of occurrence in various tissues, species and cells. Special emphasis will be attached to the evaluation of disease related pattern of glycans and differences in glycosylation prototypes.

Description of DS1-SUB3

Based on the knowledge gathered in DS1-SUB1 and the recommendation made in DS2-SUB3 the subcontractor will generate guidelines how to encode biological data to ensure reproducibility between different laboratories. The guidelines will be transformed into the database design made by the partners of DS2 and will be subsequently integrated into the P2P network.

EuroCarbDB is a Research Infrastructure Design Study Funded by the 6th Research Framework Program of the European Union
(Contract: RIDS Contract number 011952)