getOntology: Returns an instance of the ontology parser created from OWL or OBO file. Reasoning over ontologies and extracting relationships is supported by using HermiT reasoner.

Description

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

Usage

getOntology(pathToURI)

Arguments

pathToURI

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

Value

Returns an instance of the Ontology 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/

Examples

Run this code

    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)