• Development of GlyCosmos, the world’s first glycoscience portal site exhaustively integrating glycan-related omics data (Professor Kiyoko Kinoshita, Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering) Kiyoko Flora Kinoshita


Development of GlyCosmos, the world’s first glycoscience portal site exhaustively integrating glycan-related omics data (Professor Kiyoko Kinoshita, Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering) Kiyoko Flora Kinoshita

    Key Results
    ・As the world’s first glycoscience portal site, we launched GlyCosmos, which exhaustively integrates glycan-related omics data such as glycan-related genes, proteins, lipids, diseases, and pathways, and which allows users to access such various resources.
    ・Also, we developed an international glycan structure repository, as well as a repository for mass spectral data for glycomics and glycoproteomics.
    ・Glycoscience portal site representing Japan as a member of the GlySpace Alliance
    ・Portal site authorized by the Japanese Society of Carbohydrate Research

    Our research group has developed and launched GlyCosmos, the world’s first glycoscience portal site integrating omics data such as genomics, proteomics, diseases, pathways for facilitating glycoscience research. Our group is led by Professor Kiyoko Kinoshita, who is the vice president of the Glycan & Life Systems Integration Center at the Faculty of Science and Engineering, Soka University, and includes as its members: Project Leader Dr. Issaku Yamada, from the Noguchi Institute; Associate Professor Shujiro Okuda from the Niigata University Graduate School of Medical and Dental Sciences; and Dr. Hiroyuki Kaji, who is a senior researcher at the Cellular and Molecular Biotechnology Research Institute of the National Institute of Advanced Industrial Science and Technology.

    The study results were published in the scientific journal, Nature Methods, July issue, on June 22, 2020 (BST).

    The study was conducted with support from the research & development project “Construction of a Glycoscience Portal” (representative: Kiyoko Kinoshita) under the Life Science Database Integration Promotion Project (Integration Promotion Program) of the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST).

    Overview of the GlyCosmos Glycoscience Portal Site
    GlyCosmos, which allows users to access various glycan-related resources through one website, comes with the following features:
    ・User-friendly web interface facilitating the easy browsing of available information on topics such as glycan-related genes, proteins, lipids, carbohydrates, pathways, and diseases
    ・GlyTouCan international glycan structure repository and the GlycoPOST glycoproteomics repository available via GlyCosmos as its own repositories
    ・Provides data resources including integrated various glycan-related databases and data sets

    Background of the Study
    Carbohydrate chains are considered to be third-life chains, after DNA and proteins, and are involved in various biological phenomena such as in nerves, infection, immunity, and development. Due to complicated structures and biosynthesis processes, however, elucidating the functions of carbohydrate chains is more difficult compared to genome research. On the other hand, big data, accumulated through various experimental data, has drawn attention recently, and data science to exploit it has become important. The history of carbohydrate chain databases started with the development of CarbBank in the U.S. in the middle of 1990, followed by the developments of various other such databases. As related activities are occurring all over the world, researchers can technically access the information via numerous avenues. However, it has been hard for them to find their target resources. That is why GlyCosmos was developed. GlyCosmos’s beta version was published in October 2018, and upon its official launch on April 1, 2019, it was authorized as a portal site of the Japanese Society of Carbohydrate Research. Then, it was updated twice on August 2019 and April 2020 based on input from researchers involved so as to increase the types and amount of data stored and related functions, as well as to improve the user interface.

    Study Results
    The portal site, which allows users to search and browse any and all related information, focusing on carbohydrate chains but also on glycan-related genes, glycoproteins, and related diseases and pathogens, etc., from one portal site, can be used at no charge through its user-friendly web interface. Users can also access GlyTouCan*1, an international glycan structure repository to register glycan structures and have ID numbers assigned, and GlycoPOST*2, to register raw data obtained from glycan-related mass spectral experiments. Additionally, GlyCosmos has integrated domestic and international databases in addition to JCGGDB ACGG-DB*3 and GlycoNAVI*4, already developed by glycoscience researchers. Therefore, with GlyCosmos, users can browse glycan-related data in a more integrated fashion, facilitating the easy pickup of more-varied information. In addition, GlyCosmos collaborates with similar projects overseas so as to interchange and share data internationally; for example, it constitutes part of the “GlySpace Alliance” international framework for a glycoscience database with GlyGen in the U.S. and Glycomics@ExPASy in Europe.

    Future Development
    In addition to the portal site, we are going to develop various analysis tools and software to advance research & development further so as to support glycoscience researchers toward understanding biological phenomena and the further application of results involving such. Among others, we are going to proceed with the development of a database tool that makes it possible to analyze relationships between microbiomes, metabolomes, plant genomes, etc., and carbohydrate chains, which have all recently come into focus.

    Publication Information
    Scientific journal name: Nature Methods, July issue, DOI: 10.1038/s41592-020-0879-8
    Title of article: “The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences”
    Authors: Issaku Yamada, Masaaki Shiota, Daisuke Shinmachi, Tamiko Ono, Shinichiro Tsuchiya, Masae Hosoda, Akihiro Fujita, Nobuyuki P. Aoki, Yu Watanabe, Noriaki Fujita, Kiyohiko Angata, Hiroyuki Kaji, Hisashi Narimatsu, Shujiro Okuda, and Kiyoko F. Aoki-Kinoshita

    *1GlyTouCan: An international glycan structure repository storing glycan structure data; each different structure can be registered with a unique ID, from monosaccharide composition to the form of glycosidic bonds, etc.
    *2GlycoPOST: A repository for mass spectral data of carbohydrate chains and glycoproteins; upon paper publication, experimental data for the paper can be registered and published along with, for example, experimental conditions.
    *3JCGGDB, ACGG-DB: A glycan-related database developed by the National Institute of Advanced Industrial Science and Technology storing mainly data involving glycogenes, related diseases, lectins (proteins binding to carbohydrate chains), or glycoproteins
    *4GlycoNAVI: A glycan-related database developed and maintained by the Noguchi Institute, mainly storing data on the chemical synthesis of carbohydrate chains, protein recognition sites of carbohydrate chains, 3D glycan structures, and disease-related glycan structures