getOntology: Returns an instance of the ontology parser created from OWL...
In ontoCAT: Ontology traversal and search

Description Usage Arguments Value Author(s) References See Also Examples

Loads the ontology described in OWL or OBO format from the local file or on the fly by using URL.

1	getOntology(pathToURI)

pathToURI

a character string giving the URL or local name of the file to load ontology from

Returns an instance of the Ontology class.

Natalja Kurbatova

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/

Ontology and OntologyTerm

    ontologyFromURL <- getOntology("http://www.ebi.ac.uk/efo/efo.owl")
    getTermParentsById(ontologyFromURL,"EFO_0001221")
    file <- system.file("extdata", "cell.obo", package="ontoCAT")
    ontologyFromFile <- getOntology(file)
    getAllTermIds(ontologyFromFile)