simona:a Comprehensive R package for Semantic Similarity Analysis on Bio-Ontologies

Abstract

AbstractBio-ontologies are keys in structuring complex biological information for effective data integration and knowledge representation. In this paper, we presentsimona, a novel R package for semantic similarity analysis on general bio-ontolgies.Simonaimplements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. Moreover, it provides a robust toolbox supporting over 70 methods for semantic similarity analysis. Withsimona, we conduct a benchmark against current semantic similarity methods. The results demonstrate methods are clustered based on their mathematical methodologies, providing guidance for researchers in the selection of appropriate methods. Additionally, we explore annotation-based versus topology-based methods, revealing that semantic similarities solely based on ontology topology can efficiently reveal semantic similarity structures, facilitating analysis on less-studied organisms and other ontologies.Simonais freely available fromhttps://bioconductor.org/packages/simona/.