ONTTerms-class: Class "ONTTerms"

In hxin/topOnto.HDO.db: TopOnto ontology db package

Description

A class to represent Disease Ontology nodes

Objects from the Class

Objects can be created by calls of the form ONTTerms(ID, term, synonym, secondary). ID, term are required.

Slots

ID:

Object of class "character" A character string for the ontology id of a primary node.

Definition:

Object of class "character" A character string for the ontology Definition of a primary node.

Ontology:

Object of class "character" A character string for the ontology name of a primary node.

Term:

Object of class "character" A character string that defines the role of gene product corresponding to the primary ontology id.

Synonym:

Object of class "character" other ontology terms that are considered to be synonymous to the primary term attached to the ontology id. Synonymous here can mean that the synonym is an exact synonym of the primary term, is related to the primary term, is broader than the primary term, is more precise than the primary term, or name is related to the term, but is not exact, broader or narrower.

Secondary:

Object of class "character" ontology ids that are secondary to the primary ontology id as results of merging ontology terms so that One ontology id becomes the primary ontology id and the rest become the secondary.

Methods

ID

signature(object = "ONTTerms"): The get method for slot ID.

Term

signature(object = "ONTTerms"): The get method for slot Term.

Definition

signature(object = "ONTTerms"): The get method for slot Term.

Ontology

signature(object = "ONTTerms"): The get method for slot Term.

Synonym

signature(object = "ONTTerms"): The get method for slot Synonym.

Secondary

signature(object = "ONTTerms"): The get method for slot Secondary.

show

signature(x = "ONTTerms"): The method for pretty print.

Note

ONTTerms objects are used to represent primary ontology nodes in the SQLite-based annotation data package topOnto.xxx.db

Examples

ONTnode <- new("ONTTerms", ID="DOID:1234567", Term="Test", Ontology="Test", Definition="Test")
## Not run: ##I want to show an ex., but don't want to require topOnto.xxx.db
  ID(ONTnode)
  Term(ONTnode)

  ##Or you can just use these methods on a ONTTermsAnnDbBimap

  #require(DO.db)
  FirstTenBimap <- ONTTERM[1:10] ##grab the 1st ten
  Term(FirstTenBimap)

  ##Or you can just use IDs directly
  ids = keys(FirstTenBimap)
  Term(ids)

## End(Not run)

hxin/topOnto.HDO.db documentation built on May 17, 2019, 9:15 p.m.