Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed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.

Journal reference: Molecules 2021, 27, 65
DOI: 10.3390/molecules27010065

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

LIFE SCIENCES, Molecular Biology

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