getEFO: Returns an instance of the EFO ontology parser
In ontoCAT: Ontology traversal and search

Description Usage Value Author(s) References See Also Examples

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

getEFO()

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

    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)