Catherine Hayes - Towards making sense of glycan-mediated protein-protein interactions
Channel: Biocuration Conference 2023
Date: 2023-06-22

*Session:* April 26 - Community 1 - 02

*Abstract:* Research into glycobiology is fast becoming recognised as important in all fields of biology, having implications in inflammation, digestion and protection of the mucosal layer and structural integrity of proteins, among others. With the increase in publications dedicated to the solving of carbohydrate structures there is a need for well curated, annotated and searchable databases to disseminate this work. Several groups now work in fulfilling this role, and among them, Glyco@Expasy (glycoproteome.expasy.org) GlyCosmos (www.glycosomos.org) and GlyGen (www.glygen.org) have come together to create the GlySpace Alliance (www.glyspace.org), a cross-country/continent alliance to aid the glycobiology community by sharing and collaborating on glycobioinformatic resources on a FAIR basis. Each resource brings its own expertise to the collaboration with global or pairwise initiatives. Lately, the Glyco@Expasy and GlyCosmos groups have been investing efforts in linking data, through the adoption of the resource description framework and the establishment of RDF endpoints. In particular, the Glyco@Expasy side provides among others, the GlySTreeM triple store of glycan structures (glyconnect.expasy.org/glystreem/sparql) described by the GlySTreeM ontology (Daponte et al., 2021). The GlyCosmos side has its own endpoint (ts.glycosmos.org/sparql) through which the GlyTouCan glycan structure repository (www.glytoucan.org) can be accessed, among others. A key aspect to unifying resources is to make the journey between a glycoprotein (that presents one or more glycan structures) and a glycan-binding protein/lectin (that recognises one or more glycan structures) transparent and easily accessible. This sets the basis of functional glycobiology. To this end, the first step is to connect a glycan structure with its known ligand parts. This is done using a GlycoQL, a GlySTreeM-based translator tool for substructure searching (Hayes et al., 2022). It allows the creation of glycan structure queries in SPARQL and was initially tested with federated queries across UniProt and GlyConnect, the curated and annotated resource of glycoproteins of Glyco@Expasy (thousands of structures). To test the robustness of the model, it was necessary to adapt the procedure to larger data sets, such as GlyTouCan (hundred thousand entries). Collaborative work is geared towards integrating the GlySTreeM model with the rest of the GlyCosmos family of tools. By setting this up on the GlyTouCan repository the glycan structures can be identified by their GlyTouCan ID (a unique identifier) which will also facilitate the linking of multiple resources with those in the Linked Open Data universe (https://lod-cloud.net/). Examples of federated queries will be presented. Daponte, V., Hayes, C., Mariethoz, J., & Lisacek, F. (2021). Dealing with the Ambiguity of Glycan Substructure Search. Molecules, 27(1), 65. https://doi.org/10.3390/molecules27010065 Hayes, C., Daponte, V., Mariethoz, J., & Lisacek, F. (2022). This is GlycoQL. Bioinformatics, 38(Issue Supplement_2), ii162–ii167. https://doi.org/10.1093/bioinformatics/btac500