GlyTouCan 1.0--The international glycan structure repository

Abstract

Glycans are known as the third major class of biopolymers, next to DNA and proteins. They cover the surfaces of many cells, serving as the 'face' of cells, whereby other biomolecules and viruses interact. The structure of glycans, however, differs greatly from DNA and proteins in that they are branched, as opposed to linear sequences of amino acids or nucleotides. Therefore, the storage of glycan information in databases, let alone their curation, has been a difficult problem. This has caused many duplicated efforts when integration is attempted between different databases, making an international repository for glycan structures, where unique accession numbers are assigned to every identified glycan structure, necessary. As such, an international team of developers and glycobiologists have collaborated to develop this repository, called GlyTouCan and is available at http://glytoucan.org/, to provide a centralized resource for depositing glycan structures, compositions and topologies, and to retrieve accession numbers for each of these registered entries. This will thus enable researchers to reference glycan structures simply by accession number, as opposed to by chemical structure, which has been a burden to integrate glycomics databases in the past.

Figure 1.

A schematic of the Glycan Repository architecture, which comprises of the front-end web pages, a REST API interface to the relational database, and a SPARQL interface to the triplestore.

Figure 2.

The browsing functionality can filter out the results based upon motifs, monosaccharide names, monosaccharide cardinality and mass range. It is also possible to sort the results in order of accession number, contributor, mass or date entered.

Figure 3.

The glycan structure overview page displays the core structural information as well as any related data such as motifs found and monosaccharide compositions. A listing of the public databases under the Linked DB section is also displayed with links to reference the structure information directly.

Figure 4.

The methods to register a structure are by building one graphically from GlycanBuilder (8), pasting a sequence text into a form or uploading a file. The uppermost image shows the GlycanBuilder user interface. The registration confirmation screen shows an example of registering a GlycoCT (6) text sequence. The file upload method allows for registering multiple structures in a file.