Evidence map›Paper›PMID 39137905›Full record

ArticleDatabase : the journal of biological databases and curation2024

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 and 26 more

Abstract readConference Proceedings
In one paragraph

Article in Database : the journal of biological databases and curation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. O-GlcNAc informatics: advances and trends.Analytical and bioanalytical chemistry · 2025
    Review
  3. Article
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

36 authors.

Karina MartinezDepartment of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 I St. NW, Washington, DC 20052, United States.ORCID 0000-0003-2035-8459
Jon AgirreYork Structural Biology Laboratory, Department of Chemistry, University of York, Wentworth Way, York YO10 5DD, United Kingdom.ORCID 0000-0002-1086-0253
Yukie AkuneThe Glycosciences Laboratory, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, United Kingdom.ORCID 0000-0002-0839-0643
Kiyoko F Aoki-KinoshitaGlycan and Life Systems Integration Center (GaLSIC), Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan.ORCID 0000-0002-6662-8015
Cecilia ArighiDepartment of Computer and Information Sciences, University of Delaware, 18 Amstel Ave, Newark, DE 19716, United States.ORCID 0000-0002-0803-4817
Kristian B AxelsenSwiss-Prot Group, Swiss Institute of Bioinformatics (SIB), CMU, 1 rue Michel Servet, Geneva 4 1211, Switzerland.ORCID 0000-0003-3889-2879
Evan BoltonNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, United States.ORCID 0000-0002-5959-6190
Emily BordeleauMichael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada.ORCID 0009-0008-9725-6614
Nathan J EdwardsDepartment of Biochemistry and Molecular & Cellular Biology, Georgetown University, 2115 Wisconsin Ave NW, Washington, DC 20007, United States.ORCID 0000-0001-5168-3196
Elisa FaddaDepartment of Chemistry and Hamilton Institute, Maynooth University, Kilcock Road, Maynooth, Co. Kildare W23 AH3Y, Ireland.ORCID 0000-0002-2898-7770
Ten FeiziThe Glycosciences Laboratory, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, United Kingdom.ORCID 0000-0001-6495-0329
Catherine HayesProteome Informatics Group, Swiss Institute of Bioinformatics (SIB), route de Drize 7, Geneva CH-1227, Switzerland.ORCID 0000-0002-3640-3237
Callum M IvesDepartment of Chemistry and Hamilton Institute, Maynooth University, Kilcock Road, Maynooth, Co. Kildare W23 AH3Y, Ireland.
Hiren J JoshiCopenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark.ORCID 0000-0002-8192-2829
Khakurel Krishna PrasadELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, Dolní Břežany 25241, Czech Republic.
Sofia KossidaIMGT, 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.ORCID 0000-0003-2482-0022
Frederique LisacekProteome Informatics Group, Swiss Institute of Bioinformatics (SIB), route de Drize 7, Geneva CH-1227, Switzerland.ORCID 0000-0002-0948-4537
Yan LiuThe Glycosciences Laboratory, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, United Kingdom.ORCID 0000-0002-2566-6867
Thomas LüttekeInstitute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Gießen, Frankfurter Str. 100, Gießen 35392, Germany.ORCID 0000-0002-7140-9933
Junfeng MaDepartment of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3900 Reservior Road NW, Washington, DC 20007, United States.ORCID 0000-0002-5183-5425
Adnan MalikEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.ORCID 0000-0001-8123-5351
Maria MartinEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.ORCID 0000-0001-5454-2815
Akul Y MehtaDepartment of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, United States.ORCID 0000-0002-3450-3461
Sriram NeelameghamDepartments of Chemical & Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, United States.ORCID 0000-0002-1371-8500
Kalpana PanneerselvamEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.ORCID 0000-0003-2534-198X
René RanzingerComplex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States.ORCID 0000-0003-3147-448X
Sylvie Ricard-BlumInstitute 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.ORCID 0000-0001-9263-1851
Gaoussou SanouIMGT, 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.ORCID 0000-0003-2204-2466
Vijay ShankerDepartment of Computer and Information Sciences, University of Delaware, 18 Amstel Ave, Newark, DE 19716, United States.
Paul D ThomasDepartment of Population and Public Health Sciences, University of Southern California, 2001 N Soto Street, Los Angeles, CA 90032, United States.
Michael TiemeyerComplex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States.ORCID 0000-0002-8704-9143
James UrbanDepartment of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 7 B, Gothenburg 41390, Sweden.
Randi VitaImmune Epitope Database and Analysis Project, La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037, United States.ORCID 0000-0001-8957-7612
Jeet VoraDepartment of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 I St. NW, Washington, DC 20052, United States.ORCID 0000-0002-5317-1458
Yasunori YamamotoDatabase 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.ORCID 0000-0002-6943-6887
Raja MazumderDepartment of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 I St. NW, Washington, DC 20052, United States.ORCID 0000-0001-8823-9945

Funding

Gene Ontology Consortium and KnowledgebaseU24HG012212 · NHGRI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI CHRISTOPHER J MUNGALL, PAUL Warren STERNBERG · 2022 to 2026
$11.6M
Systems Biology of GlycosylationR01HL103411 · NHLBI · STATE UNIVERSITY OF NEW YORK AT BUFFALO · PI NEELAMEGHAM, SRIRAM · 2011 to 2025
$7.1M
GlyGen growth and evolution into a central resource for glycans and glycoconjugatesR24GM146616 · NIGMS · UNIVERSITY OF GEORGIA · PI Raja Mazumder, Rene Ranzinger · 2022 to 2026
$5.5M
NHGRI NIH HHS U24 HG012212NHLBI NIH HHS R01 HL103411NIGMS NIH HHS R24 GM146616NIH HHS 1R24GM146616Society for Glycobiology
6 · The paper itself

Abstract

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.

Indexed as

Data CurationPolysaccharidesBiocurationGlycosylationHumansItalyPolysaccharides

Identifiers

PMID39137905
PMCPMC11321244

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.