Noguchi Institute

To facilitate access to relevant text of literature related to data in GlyCosmos, we have developed a collection of annotated literature resources using the agile annotation method supported by the PubAnnotation system. As a proof of concept, we compiled two dictionaries for glycan motifs and epitopes, plus six additional dictionaries for relevant biological entities, covering organisms, phenotypes, diseases, and anatomical locations. Next, we collected all the PubMed abstracts from 15 selected journals, and annotated them based on these eight dictionaries. This resulted in 279,368 annotation instances made to 15,463 abstracts, meaning that we were able to automatically pull glycan motif and epitope annotations related to diseases, taxonomy, etc. from over 15,000 abstracts. All the annotations were converted into Resource Description Framework (RDF) statements to support flexible querying. For users who are not familiar with RDF, we also developed a Web interface in GlyCosmos to visualize the location of the text in publications as well as query templates to personalize queries for specific terms. Pilot searches and analyses suggest that these resources are useful for navigation of relevant contexts of biomedical associations relevant to glycobiology.

Journal Article Accepted manuscript Meeting report of the GlySpace alliance and GaLSIC symposium Get access Kiyoko F Aoki-Kinoshita, Kiyoko F Aoki-Kinoshita Glycan and Life Systems Integration Center (GaLSIC), Soka University, Tokyo 192-8677, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Frederique Lisacek, Frederique Lisacek SIB Swiss Institute of Bioinformatics & Computer Science Department, University of Geneva, Geneva, Switzerland Search for other works by this author on: Oxford Academic PubMed Google Scholar Raja Mazumder, Raja Mazumder The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States Search for other works by this author on: Oxford Academic PubMed Google Scholar Rene Ranzinger, Rene Ranzinger Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602-4712, United States Search for other works by this author on: Oxford Academic PubMed Google Scholar Michael Tiemeyer, Michael Tiemeyer Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602-4712, United States Search for other works by this author on: Oxford Academic PubMed Google Scholar Issaku Yamada, Issaku Yamada The Noguchi Institute, Tokyo 173-0003, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Nicolle H Packer Nicolle H Packer School of Natural Sciences, Macquarie University, North Ryde, Sydney, NSW 2109, Australia Corresponding author. Nicolle H. Packer, School of Natural Sciences, Macquarie University, North Ryde, Sydney, NSW 2109, Australia, [email protected] Search for other works by this author on: Oxford Academic PubMed Google Scholar Glycobiology, cwaf019, https://doi.org/10.1093/glycob/cwaf019 Published: 28 March 2025 Article history Received: 14 March 2025 Accepted: 16 March 2025 Published: 28 March 2025

Glycosylation, characterized by its complexity and diversity, is a common system across all domains of life. The glycosylation of proteins or lipids imparts them with structural and functional roles, ranging from development to infectious or Mendelian disease. The high-throughput-based omics data has revealed that glycans are involved in important cellular processes. Comprehensive knowledge of glycosylation has contributed not only to the fundamental concepts in glycoscience but also to its applications, including the development of molecular markers for diagnosis and therapeutic tools for treating diseases. The GlyCosmos Glycoscience Portal (GlyCosmos) has undergone significant updates to better support the scientific community in studying glycosylation-related phenomena. Key enhancements include the integration of expanded datasets linking glycans to other omics fields, improved tools for glycan structure prediction and analysis, and upgraded visualization capabilities to streamline data interpretation. A strengthened focus on data standardization has also been introduced, fostering interoperability between glycoscience resources and external databases. Since its release in 2019, the portal has seen a fivefold increase in user engagement, reflecting its growing relevance. These recent advancements aim to provide researchers with a more comprehensive and user-friendly platform, enabling deeper insights into glycan roles in cellular processes and disease mechanisms. GlyCosmos will continue to evolve, prioritizing community needs and advancing the integration of glycoscience with broader biological and biomedical research.Graphical Abstract