Abstract 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 less than 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/.
Urban et al. (Thu,) studied this question.
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