GlyGen data model and processing workflow.

Journal: Bioinformatics (Oxford, England)
Published Date: Jun 1, 2020

Abstract

SUMMARY: Glycoinformatics plays a major role in glycobiology research, and the development of a comprehensive glycoinformatics knowledgebase is critical. This application note describes the GlyGen data model, processing workflow and the data access interfaces featuring programmatic use case example queries based on specific biological questions. The GlyGen project is a data integration, harmonization and dissemination project for carbohydrate and glycoconjugate-related data retrieved from multiple international data sources including UniProtKB, GlyTouCan, UniCarbKB and other key resources.

Authors

  • Robel Kahsay
    The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, USA.
  • Jeet Vora
    Department of Biochemistry & Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC 20052, USA.
  • Rahi Navelkar
    Department of Biochemistry & Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC 20052, USA.
  • Reza Mousavi
    Department of Biochemistry & Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC 20052, USA.
  • Brian C Fochtman
    Department of Biochemistry & Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC 20052, USA.
  • Xavier Holmes
    Department of Biochemistry & Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC 20052, USA.
  • Nagarajan Pattabiraman
    Department of Biochemistry & Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC 20052, USA.
  • Rene Ranzinger
    Complex Carbohydrate Research Center, The University of Georgia, Athens, GA 30602, USA.
  • Rupali Mahadik
    Complex Carbohydrate Research Center, The University of Georgia, Athens, GA 30602, USA.
  • Tatiana Williamson
    Complex Carbohydrate Research Center, The University of Georgia, Athens, GA 30602, USA.
  • Sujeet Kulkarni
    Complex Carbohydrate Research Center, The University of Georgia, Athens, GA 30602, USA.
  • Gaurav Agarwal
    Departments of Endocrine & Breast Surgery, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, 226014, India. gaurav@sgpgi.ac.in.
  • Maria Martin
    European Bioinformatics Institute, Hinxton CB10 1SD, UK.
  • Preethi Vasudev
    European Bioinformatics Institute, Hinxton CB10 1SD, UK.
  • Leyla Garcia
    ZB MED Information Centre for Life Sciences, Cologne 50931, Germany.
  • Nathan Edwards
    Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20007, USA.
  • Wenjin Zhang
    Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20007, USA.
  • Darren A Natale
    Protein Information Resource, Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, D. C., United States of America.
  • Karen Ross
    Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20007, USA.
  • Kiyoko F Aoki-Kinoshita
    Faculty of Science and Engineering, Soka University, Tokyo 192-8577, Japan.
  • Matthew P Campbell
    Institute for Glycomics, Griffith University, Parklands Drive, Gold Coast, QLD, Australia.
  • William S York
    Complex Carbohydrate Research Center, The University of Georgia, Athens, GA 30602, USA.
  • Raja Mazumder
    Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States.

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