Work

This is GlycoQL

Year: 2022

Type: article

Abstract: MOTIVATION: We have previously designed and implemented a tree-based ontology to represent glycan structures with the aim of searching these structures with a glyco-driven syntax. This resulted in creating the GlySTreeM knowledge-base as a linchpin of the structural matching procedure and we now introduce a query language, called GlycoQL, for the actual implementation of a glycan structure search. RESULTS: The methodology is described and illustrated with a use-case focused on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spike protein glycosylation. We show how to enhance site annotation with federated queries involving UniProt and GlyConnect, our glycoprotein database. AVAILABILITY AND IMPLEMENTATION: https://glyconnect.expasy.org/glycoql/.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btac500

Authors: Catherine Hayes, Vincenzo Daponte, Julien Mariethoz, Frederique Lisacek

Institutions: University of Geneva, SIB Swiss Institute of Bioinformatics

Language: English

Topic: Glycosylation and Glycoproteins Research

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: National Science Foundation, Australian Government, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Staatssekretariat für Bildung, Forschung und Innovation

Awards: G2210708459, G544591541, G5489564165, Glyco-driven modelling of homeostasis in the human gut microbiome (SweetHome)