Literature DB >> 28922742

GlyTouCan: an accessible glycan structure repository.

Michael Tiemeyer1, Kazuhiro Aoki1, James Paulson2, Richard D Cummings3, William S York1, Niclas G Karlsson4, Frederique Lisacek5, Nicolle H Packer6,7, Matthew P Campbell6, Nobuyuki P Aoki8, Akihiro Fujita8, Masaaki Matsubara1, Daisuke Shinmachi8, Shinichiro Tsuchiya7, Issaku Yamada9, Michael Pierce1, René Ranzinger1, Hisashi Narimatsu10, Kiyoko F Aoki-Kinoshita8.   

Abstract

Rapid and continued growth in the generation of glycomic data has revealed the need for enhanced development of basic infrastructure for presenting and interpreting these datasets in a manner that engages the broader biomedical research community. Early in their growth, the genomic and proteomic fields implemented mechanisms for assigning unique gene and protein identifiers that were essential for organizing data presentation and for enhancing bioinformatic approaches to extracting knowledge. Similar unique identifiers are currently absent from glycomic data. In order to facilitate continued growth and expanded accessibility of glycomic data, the authors strongly encourage the glycomics community to coordinate the submission of their glycan structures to the GlyTouCan Repository and to make use of GlyTouCan identifiers in their communications and publications. The authors also deeply encourage journals to recommend a submission workflow in which submitted publications utilize GlyTouCan identifiers as a standard reference for explicitly describing glycan structures cited in manuscripts.
© The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Entities:  

Keywords:  GlyTouCan; database; glycan identifier; repository; structure

Mesh:

Substances:

Year:  2017        PMID: 28922742      PMCID: PMC5881658          DOI: 10.1093/glycob/cwx066

Source DB:  PubMed          Journal:  Glycobiology        ISSN: 0959-6658            Impact factor:   4.313


  19 in total

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Authors:  A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

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Journal:  Glycobiology       Date:  2006-02-14       Impact factor: 4.313

Review 3.  The minimum information about a proteomics experiment (MIAPE).

Authors:  Chris F Taylor; Norman W Paton; Kathryn S Lilley; Pierre-Alain Binz; Randall K Julian; Andrew R Jones; Weimin Zhu; Rolf Apweiler; Ruedi Aebersold; Eric W Deutsch; Michael J Dunn; Albert J R Heck; Alexander Leitner; Marcus Macht; Matthias Mann; Lennart Martens; Thomas A Neubert; Scott D Patterson; Peipei Ping; Sean L Seymour; Puneet Souda; Akira Tsugita; Joel Vandekerckhove; Thomas M Vondriska; Julian P Whitelegge; Marc R Wilkins; Ioannnis Xenarios; John R Yates; Henning Hermjakob
Journal:  Nat Biotechnol       Date:  2007-08       Impact factor: 54.908

4.  UniCarb-DB: a database resource for glycomic discovery.

Authors:  Catherine A Hayes; Niclas G Karlsson; Weston B Struwe; Frederique Lisacek; Pauline M Rudd; Nicolle H Packer; Matthew P Campbell
Journal:  Bioinformatics       Date:  2011-03-12       Impact factor: 6.937

5.  The minimum information required for a glycomics experiment (MIRAGE) project: sample preparation guidelines for reliable reporting of glycomics datasets.

Authors:  Weston B Struwe; Sanjay Agravat; Kiyoko F Aoki-Kinoshita; Matthew P Campbell; Catherine E Costello; Anne Dell; Stuart M Haslam; Niclas G Karlsson; Kay-Hooi Khoo; Daniel Kolarich; Yan Liu; Ryan McBride; Milos V Novotny; Nicolle H Packer; James C Paulson; Erdmann Rapp; Rene Ranzinger; Pauline M Rudd; David F Smith; Michael Tiemeyer; Lance Wells; William S York; Joseph Zaia; Carsten Kettner
Journal:  Glycobiology       Date:  2016-09-21       Impact factor: 4.313

Review 6.  KEGG as a glycome informatics resource.

Authors:  Kosuke Hashimoto; Susumu Goto; Shin Kawano; Kiyoko F Aoki-Kinoshita; Nobuhisa Ueda; Masami Hamajima; Toshisuke Kawasaki; Minoru Kanehisa
Journal:  Glycobiology       Date:  2005-07-13       Impact factor: 4.313

7.  Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans.

Authors:  Shinichiro Tsuchiya; Nobuyuki P Aoki; Daisuke Shinmachi; Masaaki Matsubara; Issaku Yamada; Kiyoko F Aoki-Kinoshita; Hisashi Narimatsu
Journal:  Carbohydr Res       Date:  2017-04-19       Impact factor: 2.104

8.  The Complex Carbohydrate Structure Database.

Authors:  S Doubet; K Bock; D Smith; A Darvill; P Albersheim
Journal:  Trends Biochem Sci       Date:  1989-12       Impact factor: 13.807

9.  GlycomeDB - integration of open-access carbohydrate structure databases.

Authors:  René Ranzinger; Stephan Herget; Thomas Wetter; Claus-Wilhelm von der Lieth
Journal:  BMC Bioinformatics       Date:  2008-09-19       Impact factor: 3.169

10.  MIRAGE: the minimum information required for a glycomics experiment.

Authors:  William S York; Sanjay Agravat; Kiyoko F Aoki-Kinoshita; Ryan McBride; Matthew P Campbell; Catherine E Costello; Anne Dell; Ten Feizi; Stuart M Haslam; Niclas Karlsson; Kay-Hooi Khoo; Daniel Kolarich; Yan Liu; Milos Novotny; Nicolle H Packer; James C Paulson; Erdmann Rapp; Rene Ranzinger; Pauline M Rudd; David F Smith; Weston B Struwe; Michael Tiemeyer; Lance Wells; Joseph Zaia; Carsten Kettner
Journal:  Glycobiology       Date:  2014-03-20       Impact factor: 4.313

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  45 in total

1.  Systems glycomics of adult zebrafish identifies organ-specific sialylation and glycosylation patterns.

Authors:  Nao Yamakawa; Jorick Vanbeselaere; Lan-Yi Chang; Shin-Yi Yu; Lucie Ducrocq; Anne Harduin-Lepers; Junichi Kurata; Kiyoko F Aoki-Kinoshita; Chihiro Sato; Kay-Hooi Khoo; Ken Kitajima; Yann Guerardel
Journal:  Nat Commun       Date:  2018-11-07       Impact factor: 14.919

2.  Application of network smoothing to glycan LC-MS profiling.

Authors:  Joshua Klein; Luis Carvalho; Joseph Zaia
Journal:  Bioinformatics       Date:  2018-10-15       Impact factor: 6.937

3.  Evolutionary conservation of human ketodeoxynonulosonic acid production is independent of sialoglycan biosynthesis.

Authors:  Kunio Kawanishi; Sudeshna Saha; Sandra Diaz; Michael Vaill; Aniruddha Sasmal; Shoib S Siddiqui; Biswa Choudhury; Kumar Sharma; Xi Chen; Ian C Schoenhofen; Chihiro Sato; Ken Kitajima; Hudson H Freeze; Anja Münster-Kühnel; Ajit Varki
Journal:  J Clin Invest       Date:  2021-03-01       Impact factor: 14.808

4.  Primary Human Natural Killer Cells Retain Proinflammatory IgG1 at the Cell Surface and Express CD16a Glycoforms with Donor-dependent Variability.

Authors:  Kashyap R Patel; Joel D Nott; Adam W Barb
Journal:  Mol Cell Proteomics       Date:  2019-08-29       Impact factor: 5.911

5.  Updates to the Symbol Nomenclature for Glycans guidelines.

Authors:  Sriram Neelamegham; Kiyoko Aoki-Kinoshita; Evan Bolton; Martin Frank; Frederique Lisacek; Thomas Lütteke; Noel O'Boyle; Nicolle H Packer; Pamela Stanley; Philip Toukach; Ajit Varki; Robert J Woods
Journal:  Glycobiology       Date:  2019-08-20       Impact factor: 4.313

6.  GlyMDB: Glycan Microarray Database and analysis toolset.

Authors:  Yiwei Cao; Sang-Jun Park; Akul Y Mehta; Richard D Cummings; Wonpil Im
Journal:  Bioinformatics       Date:  2020-04-15       Impact factor: 6.937

7.  glypy: An Open Source Glycoinformatics Library.

Authors:  Joshua Klein; Joseph Zaia
Journal:  J Proteome Res       Date:  2019-07-30       Impact factor: 4.466

8.  Standardization of PGC-LC-MS-based glycomics for sample specific glycotyping.

Authors:  Christopher Ashwood; Brian Pratt; Brendan X MacLean; Rebekah L Gundry; Nicolle H Packer
Journal:  Analyst       Date:  2019-05-08       Impact factor: 4.616

Review 9.  Applications and continued evolution of glycan imaging mass spectrometry.

Authors:  Colin T McDowell; Xiaowei Lu; Anand S Mehta; Peggi M Angel; Richard R Drake
Journal:  Mass Spectrom Rev       Date:  2021-08-15       Impact factor: 10.946

Review 10.  A Perspective on the Confident Comparison of Glycoprotein Site-Specific Glycosylation in Sample Cohorts.

Authors:  Joshua A Klein; Joseph Zaia
Journal:  Biochemistry       Date:  2019-12-31       Impact factor: 3.162

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