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Updated: Jan 8, 2026

Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions
Published on: January 20, 2022
Bridging worlds: connecting glycan representations with glycoinformatics via Universal Input and a canonicalized
James Urban1,2, Roman Joeres1,2,3,4, Daniel Bojar1,2
1Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden.
Motivation:
As the field of glycobiology has developed, so too have different glycan nomenclature systems. While each system serves specific purposes, this multiplicity creates challenges for usability, data integration, and knowledge sharing across different databases and computational tools.
Results:
We present a practical framework for automated nomenclature conversion that takes any glycan nomenclature as input without requiring declaration of the specific language and outputs a canonicalized IUPAC-condensed format as a standardized representation. Our implementation handles all common nomenclatures including WURCS, GlycoCT, IUPAC-condensed/extended, GLYCAM, CSDB-linear, LinearCode, GlycoWorkbench, GlySeeker, Oxford, and KCF, along with common typos, and manages complex cases including structural ambiguities, modifications, uncertainty in linkage information, and different compositional representations. This Universal Input framework can translate more than 10 nomenclatures in <1 ms per glycan, tested on over 150 000 sequences with 98%-100% coverage, enabling seamless integration of existing glycan databases and tools while maintaining the specific advantages of each representation system.
Availability And Implementation:
Universal Input is implemented within the glycowork Python package, available at https://github.com/BojarLab/glycowork and our web app https://canonicalize.streamlit.app/.
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