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Semantic Similarity in Bio-Ontologies

Bioconductor version: Release (3.18)

This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.

Author: Zuguang Gu [aut, cre]

Maintainer: Zuguang Gu < at>

Citation (from within R, enter citation("simona")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

01. ontology_DAG: a class for ontology data HTML R Script
02. Gene Ontology HTML R Script
03. Import ontology files HTML R Script
04. Information content HTML R Script
05. Term similarity HTML R Script
06. Similarity between two groups of terms HTML R Script
07. Visualize DAGs HTML R Script
08. Random DAGs HTML R Script
09. Shiny app HTML R Script
10. Functional enrichment HTML R Script
Reference Manual PDF


biocViews Annotation, BiomedicalInformatics, GO, Software
Version 1.0.10
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.1.0)
Imports methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions, igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize, ComplexHeatmap, grDevices, stats, utils, shiny
System Requirements Perl, Java
Bug Reports
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Suggests knitr, testthat, BiocManager, GO.db,, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png, InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment, AnnotationHub, jsonlite
Linking To Rcpp
Depends On Me
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Follow Installation instructions to use this package in your R session.

Source Package simona_1.0.10.tar.gz
Windows Binary
macOS Binary (x86_64) simona_1.0.10.tgz
macOS Binary (arm64) simona_1.0.10.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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