showHierarchyDownToTerm: Returns tree representation of term's parents

In ontoCAT: Ontology traversal and search

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

Author(s)

Natalja Kurbatova

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/

See Also

Ontology and OntologyTerm

Examples

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

ontoCAT documentation built on Nov. 17, 2017, 12:06 p.m.