Proposal: Glyco-CT Format
This documentation contains the description of a novel sequence format to encode oligosaccharides in a machine readable form.
After an evaluation of the existing sequence formats in the glycobioinformatics area we came to the conclusion that none of the existing formats suits all our needs and defines consistent solutions for the full problem-space we will encounter.
A second focus of our efforts has been the generation of a controlled vocabulary for the building blocks of oligosaccharides.
New: Version3
Download 10000 CARBBANK entries converted to GlycoCT
CARBBANK entries in GLYDE II format
During the NIH meeting 'Frontiers in Glycomics'‚ September 2006,
(http://glycomics.scripps.edu/NIHBioMarker/BioMarkerProgram.html), where all of the large world-wide carbohydrate database projects were present, the development of a robust, centralized, and thoroughly curated glycan structure database was assigned as the project with the highest priority. (see NIH-White paper)
To pave the way for a central carbohydrate structure database, the existing larger initiatives agreed to immediately start with the necessary preparatory steps for the conversion of CarbBank data into the GLYDE-II format. The result of the new conversion of CarbBank will provide a clean dataset of fully determined glycan
structures in GLYDE-II format. This data set will constitute the
state-of-the-art repertoire of available digital glycan structures.
These structures will also constitute the foundation for the future centralized database.
The files containing the conversion of CarbBank data into the GLYDE-II format can be downloaded here.
Monosaccharide Database
Carbohydrates are much more complex than other biopolymers like proteins or nucleic acids. The most often stated reason for this complexity is the fact that their single residues, the monosaccharides, can be linked in several ways, which allows the formation of branched structures. Another reason for the complexity of carbohydrates is the large number of different monosaccharides, which by far exceeds the number of amino acids (20) or nucleotides (8 [4 DNA + 4 RNA]).
Monosaccharide DB is intended to be a comprehensive resource of these monosaccharides. So far, the database contains 229 entries. These comprise the majority of the unmodified monosaccharides and several modified residues.
Due to the large number of possible modifications, it is virtually impossible to pre-fill the database with all conceivable monosaccharide residues. Therefore, the database is designed in a way that modified residues are entered and assigned a unique ID automatically on the first request.
-> Beta-Version of the Database.
Be aware, that this database is still under construction and that the ID-numbers may change until the final release.
EuroCarbDB is a Research Infrastructure Design Study
Funded by the 6th Research Framework Program of the European Union
(Contract: RIDS Contract number 011952)
