showHierarchyDownToTerm: Returns tree representation of term's parents

Description

Returns set of terms that represent ontology "opened" down to specified term, hence displaying all its parents first and then a tree level, containing specified term. Term in the set is represented as the instance of the OntologyTerm class.

Usage

showHierarchyDownToTerm(object1,object2)

Arguments

object1

instance of the Ontology class

object2

instance of the OntologyTerm class

Value

Returns set of ontology terms: each term in the set is the instance of the 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/

Examples

Run this code

    efo <- getEFO()
    term <- getTermById(efo,"EFO_0000827")
    showHierarchyDownToTerm(efo,term)