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processing of ontologies of anatomy, cell lines, and so on

Bioconductor version: Release (3.19)

Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.

Author: Vincent Carey [ctb, cre] , Sara Stankiewicz [ctb]

Maintainer: Vincent Carey <stvjc at>

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


To install this package, start R (version "4.4") 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:

ontoProc: some ontology-oriented utilites with single-cell focus for Bioconductor HTML R Script
owlents: using OWL directly in ontoProc HTML R Script
Reference Manual PDF


biocViews GO, Infrastructure, Software
Version 1.26.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License Artistic-2.0
Depends R (>= 4.0), ontologyIndex
Imports Biobase, S4Vectors, methods, stats, utils, BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph, AnnotationHub, SummarizedExperiment, reticulate, R.utils, httr
System Requirements owlready2
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Suggests knitr,,, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi
Linking To
Depends On Me SingleRBook
Imports Me pogos
Suggests Me BiocOncoTK, scDiffCom
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package ontoProc_1.26.0.tar.gz
Windows Binary
macOS Binary (x86_64) ontoProc_1.26.0.tgz
macOS Binary (arm64) ontoProc_1.26.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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