GLYDE-II: The GLYcan data exchange format

Rene Ranzinger,Krys J Kochut,John A Miller,Matthew Eavenson,Thomas Lütteke,William S York

doi:10.1016/j.pisc.2016.05.013

Rene Ranzinger, Krys J Kochut + Show 4 more

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https://doi.org/10.1016/j.pisc.2016.05.013

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Abstract

SummaryThe GLYcan Data Exchange (GLYDE) standard has been developed for the representation of the chemical structures of monosaccharides, glycans and glycoconjugates using a connection table formalism formatted in XML. This format allows structures, including those that do not exist in any database, to be unambiguously represented and shared by diverse computational tools. GLYDE implements a partonomy model based on human language along with rules that provide consistent structural representations, including a robust namespace for specifying monosaccharides. This approach facilitates the reuse of data processing software at the level of granularity that is most appropriate for extraction of the desired information. GLYDE-II has already been used as a key element of several glycoinformatics tools. The philosophical and technical underpinnings of GLYDE-II and recent implementation of its enhanced features are described.

Highlights

Glycobiology, broadly defined as the study of the structure, biosynthesis and biological functions of glycans and glycoconjugates, is an emerging field of research that has found increasing applications in diverse technologies ranging from medicine to biofuels (Varki and Sharon, 2009; Walt et al, 2012)
The development of glycomics has lagged behind genomics and proteomics in large part due to analytical challenges that stem from the structural complexity of glycans
(PARtonomy of CHeMical ENTities), which allows the structure of biological molecules to be completely and unambiguously specified at several levels of granularity

Summary

Introduction

Glycobiology, broadly defined as the study of the structure, biosynthesis and biological functions of glycans and glycoconjugates, is an emerging field of research that has found increasing applications in diverse technologies ranging from medicine to biofuels (Varki and Sharon, 2009; Walt et al, 2012). (PARtonomy of CHeMical ENTities), which allows the structure of biological molecules (including complex glycans) to be completely and unambiguously specified at several levels of granularity.

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Conclusion