ArticleBMC genomics2024
simona: a comprehensive R package for semantic similarity analysis on bio-ontologies.
Article in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Augmenting structured diagnoses through effective use of pre-trained large language models on clinical notes.JAMIA open · 2026Article
- MAPA: A Semantic Network Framework for Functional Module Discovery and Interpretation in Multi-Omics Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- MafB is a conserved transcriptional regulator of macrophage development and functional identity across tissues and species.Immunity · 2026Article
- Functional annotation of novel heat stress-responsive genes in rice utilizing public transcriptomes and structurome.Bioinformatics advances · 2026Article
- monarchr: an R package for querying biomedical knowledge graphs.Bioinformatics (Oxford, England) · 2025Article
- Astrocyte diversity and subtypes: aligning transcriptomics with multimodal perspectives.EMBO reports · 2025Review
- Sequencing validates deep learning models for EHR-based detection of Noonan syndrome in pediatric patients.NPJ genomic medicine · 2025Article
- Data- and knowledge-derived functional landscape of human solute carriers.Molecular systems biology · 2025Article
- Risk Prediction of RNA Off-Targets of CRISPR Base Editors in Tissue-Specific Transcriptomes Using Language Models.International journal of molecular sciences · 2025Article
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1 author.
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Abstract
backgroundBio-ontologies are keys in structuring complex biological information for effective data integration and knowledge representation. Semantic similarity analysis on bio-ontologies quantitatively assesses the degree of similarity between biological concepts based on the semantics encoded in ontologies. It plays an important role in structured and meaningful interpretations and integration of complex data from multiple biological domains.
resultsWe present simona, a novel R package for semantic similarity analysis on general bio-ontologies. Simona implements 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. With simona, we conducted a benchmark against current semantic similarity methods. The results demonstrate methods are clustered based on their mathematical methodologies, thus guiding researchers in the selection of appropriate methods. Additionally, we explored 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.
conclusionsSimona offers a versatile interface and efficient implementation for processing, visualization, and semantic similarity analysis on bio-ontologies. We believe that simona will serve as a robust tool for uncovering relationships and enhancing the interoperability of biological knowledge systems.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.