Terms in the Phenoscape KB fall into different general categories: entity, quality, phenotype (which typically are entity-quality compositions), and taxon. The category is sometimes needed to plug a term IRI into the right parameter for a function or API call.

term_category(x)

Arguments

x

a vector of one or more term IRIs, or a list of such IRIs or term objects (such as phenotype objects)

Value

A character vector with the term categories ("entity", "quality", "phenotype", or "taxon") of the terms in the input list.

Details

The implementation will first try infer the category from the object type and the ontology for terms of certain OBO ontologies. Where that fails it will rely subsumption by specific upper ontology terms, specifically the BFO terms "independent continuant" (for entity terms) and "quality" (for quality terms).

Examples

term_category(c("http://purl.obolibrary.org/obo/UBERON_0011618", "http://purl.obolibrary.org/obo/PATO_0002279", "http://purl.obolibrary.org/obo/VTO_0071642", "http://purl.obolibrary.org/obo/MP_0030825"))
#> [1] "entity" "quality" "taxon" "phenotype"
phens <- get_phenotypes("basihyal bone") term_category(phens$id[1:3])
#> [1] "phenotype" "phenotype" "phenotype"