ontology: Ontology for an object

In computational-metabolomics/struct: Statistics in R Using Class-based Templates

Ontology for an object

Description

All struct objects have an "ontology" slot, which is a list of ontology items for the object. The ontology method gathers ontology items from an object and all struct objects that it inherits to generate a complete list.

A base class in the struct package. Stores ontology information e.g. term, description, id etc for struct objects and provides methods for populating these fields using the 'rols' package.

A base class in the struct package. Stores multiple 'ontology_term' objects.

Usage

ontology(obj, cache = NULL)

ontology_term(
  id,
  ontology = character(),
  label = character(),
  description = character(),
  iri = character(),
  rols = TRUE
)

ontology_list(terms = list())

## S4 method for signature 'ontology_list,ANY,ANY,ANY'
x[i]

## S4 replacement method for signature 'ontology_list,ANY,ANY,ANY'
x[i] <- value

## S4 method for signature 'ontology_list'
length(x)

## S4 method for signature 'struct_class'
ontology(obj, cache = NULL)

Arguments

obj	a struct object
cache	a named list of ontology_terms for offline use. Terms from the cache are search based on the name of the list items matching the ontology id. If cache=NULL then the OLS API is used to lookup terms.
id	(character) The ontology term id e.g. 'STATO:0000555'
ontology	(character) The ontology the term is a member of e.g. 'stato'
label	(character) The label for the ontology term
description	(character) The description of the term
iri	(character) The Internationalized Resource Identifier for the term
rols	(logical) TRUE or FALSE to query the Ontology Lookup Service for missing label, description or iri if not provided as input. Default rols = TRUE
terms	A list of ontology_term objects.
x	the list
i	The list item index
value	an ontology_term() object

Value

model at the given index in the sequence

model sequence with the model at index i replaced

the number of models in the sequence

Examples

M = example_model()
ontology(M,cache=NULL)
## Not run: 
OT = ontology_term(id='STATO:0000555')

## End(Not run)
## Not run: 
OT = ontology_list(terms=list(
    ontology_term(ontology='obi',id =  'OBI:0200051'),
    ontology_term(ontology='stato',id ='STATO:0000555')
)

## End(Not run)
## Not run: 
OL = ontology_list('STATO:0000555')
OL[1]

## End(Not run)

## Not run: 
OL = ontology_list('STATO:0000555')
OL[1] = ontology_term('STATO:0000302')

## End(Not run)
## Not run: 
OL = ontology_list()
length(OL) # 0

## End(Not run)

computational-metabolomics/struct documentation built on March 27, 2024, 4:26 p.m.