Abstract
In life science fields, database integration is progressing and contributing to collaboration between different research fields, including the glycosciences. The integration of glycan databases has greatly progressed collaboration worldwide with the development of the international glycan structure repository, GlyTouCan. This trend has increased the need for a tool by which researchers in various fields can easily search glycan structures from integrated databases. We have developed a web-based glycan structure search tool, SugarDrawer, which supports the depiction of glycans including ambiguity, such as glycan fragments which contain underdetermined linkages, and a database search for glycans drawn on the canvas. This tool provides an easy editing feature for various glycan structures in just a few steps using template structures and pop-up windows which allow users to select specific information for each structure element. This tool has a unique feature for selecting possible attachment sites, which is defined in the Symbol Nomenclature for Glycans (SNFG). In addition, this tool can input and output glycans in WURCS and GlycoCT formats, which are the most commonly-used text formats for glycan structures.
Highlights
Database integration using Linked Open Data technologies [1] has been promoted in many science fields
We are collaborating with the worldwide Protein Data Bank, which recently performed an update of their data representation for carbohydrates, as a result of consultation with the glycoscience community (Carbohydrate Remediation) [5]
We describe the following as the main features of our tool: (1) an intuitive editing experience similar to GlycanBuilder; (2) editing structures and exporting of text formats supporting glycan fragments; (3) GlyTouCan database access through this tool
Summary
Database integration using Linked Open Data technologies [1] has been promoted in many science fields. GlyTouCan has over 120,000 entries registered by researchers worldwide This number is expected to increase in the future because of the release of the GlyCosmos glycoscience portal [4], which provides an integrated interface for glycoscience data, and is increasingly collaborating with other research fields to integrate glycoconjugate data, such as glycoproteins and glycolipids. We are collaborating with the worldwide Protein Data Bank (wwPDB), which recently performed an update of their data representation for carbohydrates, as a result of consultation with the glycoscience community (Carbohydrate Remediation) [5] This remediation provides access to glycan 3D structural information in the PDB in a more Findable, Accessible, Interoperable and Reusable (FAIR) manner. WURCS is included as one of the linear descriptors of carbohydrates in the PDB
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