get_term_iri: Find the IRI of the term matching a text query

In xu-hong/rphenoscape: Semantically Rich Phenotypic Traits from the Phenoscape Knowledgebase

Find the IRI of the term matching a text query

Description

Finds the term matching the query text, and returns its IRI. If the query text is already a IRI, it is returned as is.

Usage

get_term_iri(
  text,
  as,
  exactOnly = FALSE,
  nomatch = NA,
  includeRelatedSynonyms = FALSE,
  verbose = FALSE
)

Arguments

text	character. The search text to be resolved.
as	character. The ontology or ontologies as which to find the term. Can be provided in several ways: (1) IRI of the ontology; (2) the ID space for OBO ontologies such as UBERON, VTO, etc; (3) "anatomy" and "taxon" as shorthand for all anatomy and taxon ontologies, respectively; (4) NA to disable any filtering by defining ontology. Options (1) and (2) can be combined. There is no default.
exactOnly	logical. Whether to require an exact match. If TRUE, only the first exact match is returned. Default is FALSE.
nomatch	the value to return if there is no match, by default NA.
includeRelatedSynonyms	logical: optional. If TRUE when looking up the IRI, text will be matched against related synonyms as well.
verbose	logical: optional. If TRUE, prints messages prior to potentially time-consuming operations. Default is FALSE.

Details

This uses find_term to find matches, and assumes that the term of interest is a class. If there is an exact match, its IRI will be returned. If there isn't, by default partial, and as a last resort broad, matches will also be considered, although this will result in a warning.

Value

The IRI if a match is found.

xu-hong/rphenoscape documentation built on Oct. 30, 2024, 8:43 a.m.