Literature DB >> 15564307

The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures.

Norihiro Kikuchi1, Akihiko Kameyama, Shuuichi Nakaya, Hiromi Ito, Takashi Sato, Toshihide Shikanai, Yoriko Takahashi, Hisashi Narimatsu.   

Abstract

UNLABELLED: Bioinformatics resources for glycomics are very poor as compared with those for genomics and proteomics. The complexity of carbohydrate sequences makes it difficult to define a common language to represent them, and the development of bioinformatics tools for glycomics has not progressed. In this study, we developed a carbohydrate sequence markup language (CabosML), an XML description of carbohydrate structures. AVAILABILITY: The language definition (XML Schema) and an experimental database of carbohydrate structures using an XML database management system are available at http://www.phoenix.hydra.mki.co.jp/CabosDemo.html CONTACT: kikuchi@hydra.mki.co.jp.

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Year:  2004        PMID： 15564307     DOI： 10.1093/bioinformatics/bti152

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  12 in total

Review 1.  Systems glycobiology: biochemical reaction networks regulating glycan structure and function.

Authors:  Sriram Neelamegham; Gang Liu
Journal:  Glycobiology       Date:  2011-03-24       Impact factor: 4.313

2.  Glycan fingerprints: calculating diversity in glycan libraries.

Authors:  Christoph Rademacher; James C Paulson
Journal:  ACS Chem Biol       Date:  2012-03-09       Impact factor: 5.100

3.  GlycoPattern: a web platform for glycan array mining.

Authors:  Sanjay B Agravat; Joel H Saltz; Richard D Cummings; David F Smith
Journal:  Bioinformatics       Date:  2014-08-20       Impact factor: 6.937

4.  Toolboxes for a standardised and systematic study of glycans.

Authors:  Matthew P Campbell; René Ranzinger; Thomas Lütteke; Julien Mariethoz; Catherine A Hayes; Jingyu Zhang; Yukie Akune; Kiyoko F Aoki-Kinoshita; David Damerell; Giorgio Carta; Will S York; Stuart M Haslam; Hisashi Narimatsu; Pauline M Rudd; Niclas G Karlsson; Nicolle H Packer; Frédérique Lisacek
Journal:  BMC Bioinformatics       Date:  2014-01-10       Impact factor: 3.169

Review 5.  Bioinformatics and molecular modeling in glycobiology.

Authors:  Martin Frank; Siegfried Schloissnig
Journal:  Cell Mol Life Sci       Date:  2010-04-04       Impact factor: 9.261

6.  Systems-level modeling of cellular glycosylation reaction networks: O-linked glycan formation on natural selectin ligands.

Authors:  Gang Liu; Dhananjay D Marathe; Khushi L Matta; Sriram Neelamegham
Journal:  Bioinformatics       Date:  2008-10-07       Impact factor: 6.937

7.  EUROCarbDB: An open-access platform for glycoinformatics.

Authors:  Claus-Wilhelm von der Lieth; Ana Ardá Freire; Dennis Blank; Matthew P Campbell; Alessio Ceroni; David R Damerell; Anne Dell; Raymond A Dwek; Beat Ernst; Rasmus Fogh; Martin Frank; Hildegard Geyer; Rudolf Geyer; Mathew J Harrison; Kim Henrick; Stefan Herget; William E Hull; John Ionides; Hiren J Joshi; Johannis P Kamerling; Bas R Leeflang; Thomas Lütteke; Magnus Lundborg; Kai Maass; Anthony Merry; René Ranzinger; Jimmy Rosen; Louise Royle; Pauline M Rudd; Siegfried Schloissnig; Roland Stenutz; Wim F Vranken; Göran Widmalm; Stuart M Haslam
Journal:  Glycobiology       Date:  2010-11-23       Impact factor: 4.313

8.  Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de.

Authors:  Philip Toukach; Hiren J Joshi; René Ranzinger; Yuri Knirel; Claus-W von der Lieth
Journal:  Nucleic Acids Res       Date:  2007-01       Impact factor: 16.971

9.  Glycoconjugate Data Bank: Structures--an annotated glycan structure database and N-glycan primary structure verification service.

Authors:  Taku Nakahara; Ryo Hashimoto; Hiroaki Nakagawa; Kenji Monde; Nobuaki Miura; Shin-Ichiro Nishimura
Journal:  Nucleic Acids Res       Date:  2007-10-11       Impact factor: 16.971

Review 10.  Data management strategies for multinational large-scale systems biology projects.

Authors:  Wasco Wruck; Martin Peuker; Christian R A Regenbrecht
Journal:  Brief Bioinform       Date:  2012-10-09       Impact factor: 11.622
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