C. Hayes); Catherine Hayes catherine.hayes@sib.swiss 1 Vincenzo Daponte 1 Frederique Lisacek 0 1 2 Department of Computer Science, University of Geneva , Geneva, 1227 , Switzerland Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , Geneva, 1211 , Switzerland Section of Biology, University of Geneva , Geneva, 1211 , Switzerland 2023 000 0 0003

Glycosylation is a common and important post-translational modification. Using federated queries it is possible to position glycosylation in useful contexts such as glycoproteins, disease or cellular location. We present example queries to query glycan structures, glycosylated proteins and cellular location using GlySTreeM, GlyConnect and neXtProt. Glycan molecules are often found as post-translational modifications on proteins or lipids SWAT4HCLS 2023: The 14th International Conference on Semantic Web Applications and Tools for Health Care and Life

 1. Introduction

[ 1 ]. They play roles in many biological processes, such as digestion and mucosal protection [ 2, 3 ], maintenance of structural integrity of proteins [ 4 ], homing of lectins in the inflammation process [ 5 ] and the shielding of pathogenic viruses from the human immune system [ 6 ].

The biosynthesis of glycans is not template-driven; rather, it can depend on expression of hydrolases, availability of monosaccharide donors or correct protein folding. Therefore, glycan structure elucidation is quite important in understanding the role that glycans play in binding events [ 1 ]. However, comprehensive structural analysis is not always possible, and results yield heterogeneous information, from simple monosaccharide composition (monosaccharide analysis) to fully characterised structures (NMR). Liquid chromatography in tandem with mass spectrometry (LC-MS), as a standard methodology yields sequence, topology and linkage information about glycans. Even though it is often supplemented by biosynthetic knowledge and orthogonal techniques such as binding assays there may still be uncertainty in parts of the glycan.

Incomplete structures present challenges to the understanding of the precise role of glycans in binding events; structural uncertainty rules out simple structure matching. The GlySTreeM ontology was developed to describe glycan structures [ 7 ] allowing for various levels of ambiguity, in tandem with a method to translate the search input into SPARQL queries, GlycoQL [ 8 ]. We present here federated queries that show the power of GlySTreeM when used with GlyConnect and neXtProt, for querying glycosylation data in relation to proteins and disease states. Sciences ∗Corresponding author.

2. Queries

All queries can be accessed at GitHub 2.1. Query 1 From GlySTreeM give me the IDs of all the structures that contain O-linked Core 2 and at least one sialic acid and one fucose residue 2.2. Query 2 2.3. Query 3 From GlySTreeM and federated query with GlyConnect, list all glycan structures associated with IgG and the disease myositis (DOID: 633).

From GlyConnect for protein “Beta-2-glycoprotein 1”, list glycosylation sites, glycan ids found on these sites, and from neXtProt show cellular locations.

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