This is GlycoQL

Bioinformatics. 2022 Sep 16;38(Suppl_2):ii162-ii167. doi: 10.1093/bioinformatics/btac500.

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/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19*
  • Glycoproteins
  • Glycosylation
  • Humans
  • Polysaccharides / chemistry
  • SARS-CoV-2*

Substances

  • Glycoproteins
  • Polysaccharides