ontoCAT (version 1.24.0)

getAllTerms: Returns all ontology terms

Description

Returns set of ontology terms, where each term is an instance of the OntologyTerm class.

Usage

getAllTerms(object)

Arguments

object

instance of the Ontology class

Value

Returns all terms from loaded ontology as objects of OntologyTerm class.

References

Adamusiak T, Burdett T, van der Velde K J, Abeygunawardena N, Antonakaki D, Parkinson H and Swertz M: OntoCAT -- a simpler way to access ontology resources. Available from Nature Precedings http://dx.doi.org/10.1038/npre.2010.4666.1 (2010) Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H: Modeling Sample Variables with an Experimental Factor Ontology. Bioinformatics 2010, 26(8):1112--1118 Experimental Factor Ontology http://www.ebi.ac.uk/efo Ontology Common API Tasks java library http://www.ontocat.org Java sources and javadocs: http://sourceforge.net/projects/ontocat/files/

See Also

Ontology and OntologyTerm

Examples

    file <- system.file("extdata", "cell.obo", package="ontoCAT")
    ontologyFromFile <- getOntology(file)
    getAllTerms(ontologyFromFile)