preparing for a small number of entry points to owlready2 mediated by basilisk, this setup function will ingest OWL, enumerate classes and their names, and produce the 'parents' list, which can then be used with ontology_index to produce a functional ontology representation

Usage

setup_entities2(owlfn, cache_object = TRUE)

Arguments

owlfn: character(1) path to OWL file
cache_object: logical(1) if TRUE, cache the `ontology_index` instance in BiocFileCache::BiocFileCache()

Note

Production of an `ontology_index` instance will often throw a warning when "Thing" is part of the ontology. suppressWarnings has been used in the code to suppress this. This may be too aggressive an approach.

Examples

pa = get_ordo_owl_path()
orde = setup_entities2(pa)
orde
#> Ontology with 15239 terms
#> 
#> Properties:
#> 	id: character
#> 	name: character
#> 	parents: list
#> 	children: list
#> 	ancestors: list
#> 	obsolete: logical
#> Roots:
#> 	Orphanet_C010 - genetic material
#> 	Orphanet_C001 - clinical entity
#> 	Orphanet_C041 - inactive clinical entity
#> 	4.0 - CC BY 4.0