Development of Carbohydrate Nomenclature and Representation

This chapter offers a general background for researchers embarking in glycoscience to grasp the evolution and present status of the nomenclature(s) and representation(s) of glycans and complex carbohydrates. The availability of high-performance computing and the application of data mining are opening new paths to discovery. The field of structural glycobiology has benefited from such advances with the development of tools and databases for the structural and functional analysis of carbohydrates. There is a need to conform to the recommendations of nomenclatures of carbohydrates while the constraints are required by the developing field of glycobiology in terms of visualization and encoding. The present chapter describes the nomenclatures, symbols, and presentations that form part of the “language” used to communicate more effectively and used in different databases. Besides, some issues related to the interoperability of glycan databases throughout glycan databases are also addressed. The semantic web approach promotes further the description and integration of structural and experimental metadata throughout the development of ontologies for domain knowledge representation.

[1]  M F Sanner,et al.  Python: a programming language for software integration and development. , 1999, Journal of molecular graphics & modelling.

[2]  Martin Frank,et al.  GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. , 2006, Glycobiology.

[3]  Emil Fischer, His Personality, His Achievements, and His Scientific Progeny , 2002 .

[4]  Tatsuya Akutsu,et al.  KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains , 2004, Nucleic Acids Res..

[5]  W. Haworth.  The constitution of sugars , 2022 .

[6]  Kiyoko F Aoki-Kinoshita,et al.  The RINGS resource for glycome informatics analysis and data mining on the Web. , 2010, Omics : a journal of integrative biology.

[7]  Yaniv Altshuler,et al.  Glycoforum a Novel Linear Code ® Nomenclature for Complex Carbohydrates , 2022 .

[8]  E. Fischer,et al.  Synthesen in der Zuckergruppe II , 1890 .

[9]  J. Bijvoet,et al.  Determination of the Absolute Configuration of Optically Active Compounds by Means of X-Rays , 1951, Nature.

[10]  Serge Pérez,et al.  POLYS 2.0: An open source software package for building three‐dimensional structures of polysaccharides , 2014, Biopolymers.

[11]  Yue Mao,et al.  CarbBuilder: An Adjustable Tool for Building 3D Molecular Structures of Carbohydrates for Molecular Simulation , 2011, 2011 IEEE Seventh International Conference on eScience.

[12]  John E Stone,et al.  Visualisation of cyclic and multi-branched molecules with VMD. , 2009, Journal of molecular graphics & modelling.

[13]  Martin Frank,et al.  Bioinformatics and molecular modeling in glycobiology , 2010, Cellular and Molecular Life Sciences.

[14]  Laurent Nahon,et al.  Ribose and related sugars from ultraviolet irradiation of interstellar ice analogs , 2016, Science.

[15]  Louise Royle,et al.  Proposal for a standard system for drawing structural diagrams of N‐ and O‐linked carbohydrates and related compounds , 2009, Proteomics.

[16]  David Weininger,et al.  SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..

[17]  Alessio Ceroni,et al.  The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures , 2007, Source Code for Biology and Medicine.

[18]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[19]  C. W. von der Lieth,et al.  LINUCS: linear notation for unique description of carbohydrate sequences. , 2001, Carbohydrate research.

[20]  S. Kornfeld,et al.  The synthesis of complex-type oligosaccharides. II. Characterization of the processing intermediates in the synthesis of the complex oligosaccharide units of the vesicular stomatitis virus G protein. , 1978, The Journal of biological chemistry.

[21]  Toshihide Shikanai,et al.  The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures , 2005, Bioinform..

[22]  Evan Bolton,et al.  An overview of the PubChem BioAssay resource , 2009, Nucleic Acids Res..

[23]  Thomas Wetter,et al.  GlycomeDB – integration of open-access carbohydrate structure databases , 2008, BMC Bioinformatics.

[24]  Marc Baaden,et al.  Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: a video game-based computer graphic software. , 2015, Glycobiology.

[25]  C. Lieth,et al.  GlycoCT-a unifying sequence format for carbohydrates. , 2008, Carbohydrate research.

[26]  Evan Bolton,et al.  Symbol Nomenclature for Graphical Representations of Glycans. , 2015, Glycobiology.

[27]  Haruki Nakamura,et al.  Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.

[28]  Michelle Kuttel,et al.  Techniques for visualization of carbohydrate molecules. , 2006, Journal of molecular graphics & modelling.

[29]  Oliver Horlacher,et al.  Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search , 2015, PloS one.

[30]  William S York,et al.  GLYDE-an expressive XML standard for the representation of glycan structure. , 2005, Carbohydrate research.

[31]  Serge Pérez,et al.  Conformations of the hydroxymethyl group in crystalline aldohexopyranoses , 1979 .

[32]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[33]  Alan D. McNaught.  Nomenclature of carbohydrates , 1997 .

[34]  Philip V. Toukach,et al.  Bacterial Carbohydrate Structure Database 3: Principles and Realization , 2011, J. Chem. Inf. Model..

[35]  Michael Darsow,et al.  ChEBI: a database and ontology for chemical entities of biological interest , 2007, Nucleic Acids Res..

[36]  K. Bretonnel Cohen,et al.  BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains , 2014, Journal of Biomedical Semantics.

[37]  Roger A. Laine,et al.  Invited Commentary: A calculation of all possible oligosaccharide isomers both branched and linear yields 1.05 × 1012 structures for a reducing hexasaccharide: the Isomer Barrier to development of single-method saccharide sequencing or synthesis systems , 1994 .

[38]  Philip V. Toukach,et al.  Introducing glycomics data into the Semantic Web , 2013, J. Biomed. Semant..

[39]  Robert M. Hanson,et al.  Jmol – a paradigm shift in crystallographic visualization , 2010 .

[40]  Carolyn R. Bertozzi,et al.  Essentials of Glycobiology , 1999 .