Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy

Karina Martinez; Jon Agirre; Yukie Akune; Kiyoko F Aoki-Kinoshita; Cecilia Arighi; Kristian B Axelsen; Evan Bolton; Emily Bordeleau; Nathan J Edwards; Elisa Fadda; Ten Feizi; Catherine Hayes; Callum M Ives; Hiren J Joshi; Khakurel Krishna Prasad; Sofia Kossida; Frederique Lisacek; Yan Liu; Thomas Lütteke; Junfeng Ma; Adnan Malik; Maria Martin; Akul Y Mehta; Sriram Neelamegham; Kalpana Panneerselvam; René Ranzinger; Sylvie Ricard-Blum; Gaoussou Sanou; Vijay Shanker; Paul D Thomas; Michael Tiemeyer; James Urban; Randi Vita; Jeet Vora; Yasunori Yamamoto; Raja Mazumder

doi:10.1093/database/baae073

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Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy

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Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy

Karina Martinez, Jon Agirre, Yukie Akune, Kiyoko F Aoki-Kinoshita, Cecilia Arighi, Kristian B Axelsen, Evan Bolton, Emily Bordeleau, Nathan J Edwards, Elisa Fadda, …

Database : the journal of biological databases and curation, Vol.2024, baae073

13/08/2024

DOI: https://doi.org/10.1093/database/baae073

PMID: 39137905

Résumé

Biocuration

Data Curation - methods

Glycosylation

Humans

Italy

Polysaccharides - metabolism

Dynamic changes in protein glycosylation impact human health and disease progression. However, current resources that capture disease and phenotype information focus primarily on the macromolecules within the central dogma of molecular biology (DNA, RNA, proteins). To gain a better understanding of organisms, there is a need to capture the functional impact of glycans and glycosylation on biological processes. A workshop titled "Functional impact of glycans and their curation" was held in conjunction with the 16th Annual International Biocuration Conference to discuss ongoing worldwide activities related to glycan function curation. This workshop brought together subject matter experts, tool developers, and biocurators from over 20 projects and bioinformatics resources. Participants discussed four key topics for each of their resources: (i) how they curate glycan function-related data from publications and other sources, (ii) what type of data they would like to acquire, (iii) what data they currently have, and (iv) what standards they use. Their answers contributed input that provided a comprehensive overview of state-of-the-art glycan function curation and annotations. This report summarizes the outcome of discussions, including potential solutions and areas where curators, data wranglers, and text mining experts can collaborate to address current gaps in glycan and glycosylation annotations, leveraging each other's work to improve their respective resources and encourage impactful data sharing among resources. Database URL: https://wiki.glygen.org/Glycan_Function_Workshop_2023.

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Titre: Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy
Créateurs - sans rôle: Karina Martinez - Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 I St. NW, Washington, DC 20052, United States
Jon Agirre - York Structural Biology Laboratory, Department of Chemistry, University of York, Wentworth Way, York YO10 5DD, United Kingdom
Yukie Akune - The Glycosciences Laboratory, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, United Kingdom
Kiyoko F Aoki-Kinoshita - Glycan and Life Systems Integration Center (GaLSIC), Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
Cecilia Arighi - Department of Computer and Information Sciences, University of Delaware, 18 Amstel Ave, Newark, DE 19716, United States
Kristian B Axelsen - Swiss-Prot Group, Swiss Institute of Bioinformatics (SIB), CMU, 1 rue Michel Servet, Geneva 4 1211, Switzerland
Evan Bolton - National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, United States
Emily Bordeleau - Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
Nathan J Edwards - Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, 2115 Wisconsin Ave NW, Washington, DC 20007, United States
Elisa Fadda - Department of Chemistry and Hamilton Institute, Maynooth University, Kilcock Road, Maynooth, Co. Kildare W23 AH3Y, Ireland
Ten Feizi - The Glycosciences Laboratory, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, United Kingdom
Catherine Hayes - Proteome Informatics Group, Swiss Institute of Bioinformatics (SIB), route de Drize 7, Geneva CH-1227, Switzerland
Callum M Ives - Department of Chemistry and Hamilton Institute, Maynooth University, Kilcock Road, Maynooth, Co. Kildare W23 AH3Y, Ireland
Hiren J Joshi - Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
Khakurel Krishna Prasad - ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, Dolní Břežany 25241, Czech Republic
Sofia Kossida - IMGT, The International ImMunoGeneTics Information System, National Center for Scientific Research (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), 141 rue de la Cardonille, Montpellier 34 090, France
Frederique Lisacek - Proteome Informatics Group, Swiss Institute of Bioinformatics (SIB), route de Drize 7, Geneva CH-1227, Switzerland
Yan Liu - The Glycosciences Laboratory, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, United Kingdom
Thomas Lütteke - Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Gießen, Frankfurter Str. 100, Gießen 35392, Germany
Junfeng Ma - Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3900 Reservior Road NW, Washington, DC 20007, United States
Adnan Malik - European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
Maria Martin - European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
Akul Y Mehta - Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, United States
Sriram Neelamegham - Departments of Chemical & Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, United States
Kalpana Panneerselvam - European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
René Ranzinger - Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States
Sylvie Ricard-Blum - Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, University Lyon 1, CNRS, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex F-69622, France
Gaoussou Sanou - IMGT, The International ImMunoGeneTics Information System, National Center for Scientific Research (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), 141 rue de la Cardonille, Montpellier 34 090, France
Vijay Shanker - Department of Computer and Information Sciences, University of Delaware, 18 Amstel Ave, Newark, DE 19716, United States
Paul D Thomas - Department of Population and Public Health Sciences, University of Southern California, 2001 N Soto Street, Los Angeles, CA 90032, United States
Michael Tiemeyer - Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States
James Urban - Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 7 B, Gothenburg 41390, Sweden
Randi Vita - Immune Epitope Database and Analysis Project, La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037, United States
Jeet Vora - Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 I St. NW, Washington, DC 20052, United States
Yasunori Yamamoto - Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan
Raja Mazumder - Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 I St. NW, Washington, DC 20052, United States
Détails de publication: Database : the journal of biological databases and curation, Vol.2024, baae073
Note de subvention: 1R24GM146616 / NIH HHS R24 GM146616 / NIGMS NIH HHS R01 HL103411 / NHLBI NIH HHS U24 HG012212 / NHGRI NIH HHS Society for Glycobiology
Identifiants: 99139803909311
Unité académique: Institut de Génétique Humaine - IGH
Langue: English
Type de ressource: Journal article