GlycoAudit: structural joinability and annotation degree shape glycan–agent relation ranking

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ID: 333067
2026
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Abstract
Abstract Motivation Benchmark scores can be misleading when identifier resolution, structural availability, and incomplete interaction annotation determine which glycans can be evaluated. GlycoAudit audits this evidence-to-structure path before model comparison. Results A strict accession, branch, and sequence contract retained 44 of 173 resolved SugarBind glycans (25.4%) and excluded 129 (74.6%). The joined domain was substantially more densely annotated. Under leakage-controlled held-out-positive ranking, the Web3 Unique Representation of Carbohydrate Structures (WURCS) exceeded the evaluated global structural summaries. Yet a leave-one-agent-out annotation-degree control achieved higher mean reciprocal rank (0.491 versus 0.381) and higher known-positive average precision (APknown), 0.489 versus 0.373, whereas WURCS achieved higher Recall@5 (0.688 versus 0.456). These metric-dependent reversals show that structural joinability, annotation degree, candidate construction, and evaluation choice jointly shape apparent benchmark performance. The release evaluates positive-relation ranking, not confirmed non-binding classification or cross-source transfer. Availability GlycoAudit makes evidence, joining decisions, exclusions, candidates, folds, controls, and machine-readable results inspectable in the public GlycoAudit repository.
Reference Key
openalex_W7223028719 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Minqi Chen, Minrui Chen, Guanjie Zou, Lunxu Liu
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Journal Bioinformatics advances
Year 2026
DOI
10.1093/bioadv/vbag308
URL
https://doi.org/10.1093/bioadv/vbag308
Keywords Keywords not found

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