new_mapping: Add a new mapping to an ontology
In ontologics: Code-Logics to Handle Ontologies

new_mapping

R Documentation

Add a new mapping to an ontology

Description

Extend an ontology by creating mappings between classes and concepts of external vocabularies and the harmonised classes and concepts.

Usage

new_mapping(
  new = NULL,
  target,
  source = NULL,
  lut = NULL,
  match = NULL,
  certainty = NULL,
  type = "concept",
  ontology = NULL,
  verbose = FALSE,
  beep = NULL
)

Arguments

`new`	`character(.)` the english external label(s) that shall be mapped to labels that do already exist in the ontology.
`target`	`data.frame(.)` the already harmonised English label(s) to which the external labels shall be mapped; derive with get_concept().
`source`	`character(1)` any character uniquely identifying the source dataset of the new label.
`lut`	`character(.)` in case the terms used for mapping are from a look up table (i.e. a standardised set of terms with a description), provide this table with column names 'label' and 'description' here.
`match`	`character(1)` the skos mapping property used to describe the link, possible values are `"close"`, `"exact"`, `"broad"` and `"narrow"`.
`certainty`	`integerish(1)` the certainty of the match. Possible values are between 1 and 4, with meaning 1 = probably unreliable 2 = unclear, assigned according to a given definition 3 = clear, assigned according to a given definition 4 = original, harmonised term (can't be assigned by a user) .
`type`	`character(1)` whether the new labels are mapped to a `"concept"`, or to a `"class"`.
`ontology`	`ontology(1)` either a path where the ontology is stored, or an already loaded ontology.
`verbose`	`logical(1)` whether or not to give detailed information on the process of this function.
`beep`	`integerish(1)` Number specifying what sound to be played to signal the user that a point of interaction is reached by the program, see `beep`.

Value

No return value, called for the side effect of adding new mappings to an ontology.

Examples

ontoDir <- system.file("extdata", "crops.rds", package = "ontologics")
onto <- load_ontology(path = ontoDir)

mapping <- data.frame(old = c("BIOENERGY CROPS", "Bioenergy woody",
                              "Other bioenergy crops"),
                      new = c("bioenergy plants", "Wood plantation for fuel",
                              "Algae for bioenergy"),
                      type = c("close", "broader", "broader"))

onto <- new_source(name = "externalDataset",
                   version = "0.0.1",
                   description = "a vocabulary",
                   homepage = "https://www.something.net",
                   license = "CC-BY-0",
                   ontology = onto)

onto <- get_concept(label = mapping$old, ontology = onto) %>%
  new_mapping(new = mapping$new,
              target = .,
              match = mapping$type,
              source = "externalDataset",
              certainty = 3,
              ontology = onto)

ontologics documentation built on May 31, 2023, 6:53 p.m.