Design studies
Design Study 1:
The predefinition of standard representations of both the methods used and the data generated in glycobiology / glycomics studies, guidelines for good practice, establishment of procedures for quality control and the development of associated data base models will be the main subject of the DS1 task.
Objectives
- Definition of a minimum description of glycomics experiments (DS1-T1 to DS1-T4, DS1-SUB1)
- Guidelines for good practice and quality control (DS1-T4, DS1-SUB3)
- Convention for encoding metadata such as taxonomy, physicochemical properties, biological functions (sub-tasks DS1-T1, DS1-T2 and DS1-T3, DS1-SUB3)
- Definition of a broadly accepted representation of carbohydrate structures (sub-tasks DS1-T2, DS1-T3, DS1-T6)
- Creation of a system of registry numbers for carbohydrate structures (sub-tasks DS1-T5)
- Maintaining EUROCarbDB the virtual communication centre (relevant for all sub-tasks)
Design Study 2:
DS2 implies the design of
software tools, which enable a peer-to-peer network of distributed
databases for glycosciences. The availability of such a tool will
encourage people to input their recorded experimental data into a local
database that may be kept private until it is published. Inexpensive
hardware platforms and the availability of free software tools will
favour this process.
Objectives
- Feasibility study and technical preparatory work for a peer-to-peer network of distributed databases for applications related to glycosciences (DS2-T1, DS2-T2, DS2-T4, DS2-T6).
- Feasibility study for automatic cross-referencing and linking with existing genomics and proteomics databases (DS2-T4, DS2-T6, DS2-SUB2, DS2-SUB4)
- Implementation of a prototype of a peer-to-peer network and the central database at EMBL-EBI to ensure sustainability of the project (DS2-T4, DS2-T5, DS2-T6).
Design Study 3
DS3 will support the development of algorithms, which enable a rapid and reliable automatic interpretation of mass spectrometry (MS) and HPLC data. The existence of sufficiently large high quality collections of reference spectra is an urgent demand of ongoing high throughput glycomics projects. The existence of an accepted depository for glyco-related spectroscopic data will guarantee that the loss of primary data can be considerably reduced.
Objectives
- Creation of common standards for MS- and HPLC data (DS3-T1, DS3-T2)
- Creation of procedures and algorithms for the automatic inclusion of MS spectra and HPLC profiles into the prototype database (DS3-T3, DS3-T4).
- Feasibility study how reliably calculated fragmentation patterns derived online from glycan sequences enable a safe automatic assignment of mass spectra (DS3-T5, DS3-T7). " Feasibility study how reliably HPLC profiles can be used enable a safe automatic annotation of glycans (DS3-T5, DS3-T7).
- Preparation of manuals, tutorials and guideline for user input and retrieval options (DS3-T6).
Design Study 4
DS4 will support the development of
algorithms, which enable a rapid and reliable automatic interpretation
of nuclear magnetic resonance
(NMR) spectra. The existence of sufficiently large high quality
collections of reference spectra is an urgent demand of ongoing high
throughput glycomics projects. The existence of an accepted depository
for glyco-related spectroscopic data will guarantee that the loss of
primary data can be considerably reduced.
Objectives
- Creation of a common standard for NMR-spectra and related experimental data (DS4-T1, DS4- T2, DS4-T3)
- Creation of procedures and algorithms for the automatic inclusion of NMR spectra P2P network (DS3-T3).
- Development of algorithms for automatic NMR-spectra interpretation. (DS4-T4)
- Feasibility study of the reliably of the automatic assignment procedures (DS4-T6).
- Preparation of manuals and tutorials for NMR tools and databases (DS4-T5).
EuroCarbDB is a Research Infrastructure Design Study
Funded by the 6th Research Framework Program of the European Union
(Contract: RIDS Contract number 011952)
