OWL Objects — owl • rphenoscape

as.owl creates an object (or a list of objects) of type "owl". The object to be coerced must be a character vector. The character vector must be a valid OWL expression appropriate for the format. The object returned will have a type appropriate for the format.

is.owl tests whether an object is of type "owl"

is.manchester_owl tests whether an object is of type "owlmn"

as.owl(owlstr, format = "manchester", usesLabels = FALSE)

is.owl(x)

is.manchester_owl(x)

Arguments

owlstr: a valid OWL expression for the chosen format
format: the OWL syntax to which owlstr conforms - currently only "manchester" (for OWL Manchester Syntax) is allowed which applies the "owlmn" type to the returned object
usesLabels: logical. If TRUE the owlstr parameter must contain a label-based class expression to be resolved into OWL Manchester expression composed of IRIs. Labels containing spaces must be single-quoted, e.g. 'basihyal bone'. Exact label matches will be resolved to term identifiers. Default is FALSE.
x: an object to check

Value

as.owl returns an object of type "owl" and a format specific type such as "owlmn", or a list of such objects. Note that (at least currently) these are in essence character strings, and are recognizable as such by R.

is.owl returns TRUE if the object is of type "owl" and FALSE otherwise.

is.manchester_owl returns TRUE if the object is of type "owlmn" and FALSE otherwise.

Details

Create objects of type "owl" that represent OWL expressions.

Examples

as.owl("<http://purl.obolibrary.org/obo/VTO_0034991> 
        or <http://purl.obolibrary.org/obo/VTO_0037519>")
#> [1] "<http://purl.obolibrary.org/obo/VTO_0034991> \n        or <http://purl.obolibrary.org/obo/VTO_0037519>"
#> attr(,"class")
#> [1] "owl"       "owlmn"     "character"
as.owl("Characiformes or Siluriformes", usesLabels = TRUE)
#> [1] "<http://purl.obolibrary.org/obo/VTO_0034991> or <http://purl.obolibrary.org/obo/VTO_0037519>"
#> attr(,"class")
#> [1] "owl"       "owlmn"     "character"
obj <- as.owl("'fin spine' and ('part of' some 'fin spine')", usesLabels = TRUE)
obj
#> [1] "<http://purl.obolibrary.org/obo/UBERON_4200075> and (<http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/UBERON_4200075>)"
#> attr(,"class")
#> [1] "owl"       "owlmn"     "character"
is.character(obj)
#> [1] TRUE