The ontoCAT package provides a simple interface to the Experimental Factor Ontology (EFO) and to any other ontology described in OWL or OBO format.

Description

The ontoCAT package provides a simple interface to the Experimental Factor Ontology (http://www.ebi.ac.uk/efo) and to any other ontology described in OWL or OBO format.

Package can load the ontology from a local file or on the fly from a URL and internally create the inferred ontology view. Experimental Factor Ontology (EFO) is the default ontology, loaded from: http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/InferredEFOOWLview/EFO_inferred.owl. The package's methods allow to parse an ontology, search terms in it, find out term parents and children. The package is based on the Ontology Common API Tasks Java library (http://www.ontocat.org) as well as various other utilites methods and depends on rJava R package.

Details

Package: ontoCAT
Type: Package
Version: 1.0.0
Date: 2010-09-20
License: Apache License
LazyLoad: yes

Author(s)

Natalja Kurbatova <natalja@ebi.ac.uk>

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, OntologyTerm, getOntology and getEFO

Examples

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    efo<-getEFO()
    file <- system.file("extdata", "cell.obo", package="ontoCAT")
    ontology <- getOntology(file)

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