Package: ontologyIndex 2.12

ontologyIndex: Reading Ontologies into R

Functions for reading ontologies into R as lists and manipulating sets of ontological terms - 'ontologyX: A suite of R packages for working with ontological data', Greene et al 2017 <doi:10.1093/bioinformatics/btw763>.

Authors:Daniel Greene <[email protected]>

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ontologyIndex.pdf |ontologyIndex.html✨
ontologyIndex/json (API)
NEWS

# Install 'ontologyIndex' in R:

install.packages('ontologyIndex', repos = c('https://daniel-jg.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

go - GO index
hpo - HPO index
mpo - MPO index

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

7.35 score 6 stars 28 packages 376 scripts 2.0k downloads 3 mentions 16 exports 0 dependencies

Last updated from:0c16aa8649. Checks:8 OK, 1 NOTE. Indexed: yes.

Target	Result	Total time
linux-devel-x86_64	OK	106
source / vignettes	OK	133
linux-release-x86_64	OK	106
macos-devel-arm64	OK	137
macos-release-arm64	OK	94
windows-devel	OK	68
windows-release	OK	67
windows-oldrel	NOTE	90
wasm-release	OK	61

Exports:check exclude_descendants get_ancestors get_descendants get_OBO get_ontology get_relation_names get_term_descendancy_matrix get_term_frequencies get_term_info_content get_term_property intersection_with_descendants minimal_set ontology_index propagate_relations prune_descendants

Dependencies:

Creating an ontology_index

Daniel Greene

Rendered fromreading-ontologies.Rmdusingknitr::rmarkdownon Feb 15 2026.

Last update: 2022-08-15
Started: 2016-10-28

Introduction to ontologyX

Daniel Greene

Rendered fromintro-to-ontologyX.Rmdusingknitr::rmarkdownon Feb 15 2026.

Last update: 2022-08-15
Started: 2016-10-28

Citation

Readme and manuals

Help Manual

Help page	Topics
Functions for Reading Ontologies into R	ontologyIndex-package ontologyIndex
Case 'ontology_index' object to 'data.frame'	as.data.frame.ontology_index
Check an ontology index object	check
Exclude terms descending from any in a given set of root terms	exclude_descendants
Get set of terms containing all ancestors of terms in a given set	get_ancestors
Get set of terms containing all descendants of terms in a given set	get_descendants
Read ontology from OBO file into R	get_OBO get_ontology
Get names of relations used in OBO file	get_relation_names
Get logical descendancy matrix for set of terms	get_term_descendancy_matrix
Get frequency of each term in a set of phenotypes	get_term_frequencies
Get information content of each term in a set of phenotypes	get_term_info_content
Get property of individual ontological term	get_term_property
GO index	go
HPO index	hpo
Intersect a set of terms with the descendants of a given set of roots	intersection_with_descendants
Remove redundant/implied terms from a set of terms	minimal_set
MPO index	mpo
Create 'ontology_index' object from vectors and lists of term properties	ontology_index
Print 'ontology_index' object	print.ontology_index
Select terms by propagating relations from a set of terms	propagate_relations
Exclude terms descending from a given set of roots but include those roots which were originally implicitly present.	prune_descendants