Article
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Preserved in Portico This version is not peer-reviewed
Dealing with the Ambiguity of Glycan Substructure Search
Version 1
: Received: 2 November 2021 / Approved: 5 November 2021 / Online: 5 November 2021 (08:34:05 CET)
A peer-reviewed article of this Preprint also exists.
Daponte, V.; Hayes, C.; Mariethoz, J.; Lisacek, F. Dealing with the Ambiguity of Glycan Substructure Search. Molecules 2022, 27, 65. Daponte, V.; Hayes, C.; Mariethoz, J.; Lisacek, F. Dealing with the Ambiguity of Glycan Substructure Search. Molecules 2022, 27, 65.
Abstract
The level of ambiguity in describing glycan structure has significantly increased with the upsurge of large scale glycomics and glycoproteomics experiments. Consequently, an ontology-based model appears as an appropriate solution for navigating this data. However, navigation is not sufficient and the model should also enable advanced search and comparison. A new ontology with a tree logical structure is introduced to represent glycan structures irrespective of the precision of molecular details. The model heavily relies on the GlycoCT encoding of glycan structures. Its implementation in the GlySTreeM knowledge base was validated with GlyConnect data and benchmarked with the Glycowork library. GlySTreeM is shown to be fast, consistent, reliable and more flexible than existing solutions for matching parts of or whole glycan structures. The model is also well suited to painless future expansion. Availability:https://glyconnect.expasy.org/glystreem/wiki
Keywords
Glycan structure; Knowledge representation; Pattern recognition; Ontology; Semantic web
Subject
Biology and Life Sciences, Biochemistry and Molecular Biology
Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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