getEFO: Returns an instance of the EFO ontology parser

Description

Loads the latest EFO version on the fly, creating the inferred ontology classes.

Usage

getEFO()

Arguments

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

    efo<-getEFO()
    getEFOBranchRootIds(efo)
    getTermParentsById(efo,"EFO_0001221")
    term_efo <- getTermById(efo,"EFO_0004902")
    isEFOBranchRoot(efo,term_efo)
    searchTermPrefix(efo,"leuk")    
    getTermAndAllChildren(efo,term_efo)