Functions for 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 .


ontologyIndex 2.2

  • The *_branches functions have all been renamed to *_descendants and their branch_roots argument to roots.
  • The get_descendants function has had two arguments renamed: ancestor is now roots and can accept a vector of root terms, returning the set of all terms which descend from them; remove_ancestor is now exclude_roots, determining whether or not to exclude the given roots terms from the result.
  • A check function which checks whether an ontology is valid has been added.
  • XML encoded 'OWL' files can now be read in as ontology_indexes.

ontologyIndex 2.1

  • A specialisation of print has been added for ontology_indexes.

ontologyIndex 2.0

  • get_ontology now only requires a file argument.
  • ontology_index objects now contain an obsolete slot - a logical vector.
  • prune_branches, exclude_branches and intersection_with_branches now use the same signature and are renamed to reflect the possibilit of passing multiple branch roots.
  • get_term_property, get_term_parents, get_term_ancestors and get_term_children functions with as_names argument to get descriptive names added for convenience.
  • swap_out_alt_ids replaced with force_compatibility which optionally throws an error if non-matchable term IDs are passed.
  • GO now included: data(go) now loads an ontology_index of the Gene Ontology (2015-11-27).

Reference manual

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2.7 by Daniel Greene, 8 months ago

Browse source code at

Authors: Daniel Greene <[email protected]>

Documentation:   PDF Manual  

GPL (>= 2) license

Suggests knitr, rmarkdown

Imported by PTXQC, SimReg, gsEasy, ontologyPlot, ontologySimilarity.

Depended on by ontoFAST.

Suggested by scDiffCom.

See at CRAN