ontoCAT R package for ontologies traversal and search

An R package called ''ontoCAT'' provides a simple interface to any ontology described in OWL or OBO formats. The ontoCAT R package supports these two formats widely used for ontology creation and provides unified, format independent access to the ontology terms and ontology hierarchy. Our package's focus is the basic methods that allows ontology traversal and search: search of the terms, getting paticular term's parents and/or children, showing paths to the term from the root element of the ontology, showing flat tree representations of the ontology hierarchy, list and search of relations, etc. Additional functionality of the ontoCAT R package allows to work with group of ontologies and with the major ontology repositories like OLS and Bioportal, namely search terms within batch of ontologies, list available ontologies and load selected ontology for futher analysis when needed. The ontoCAT R package has been used in a number of projects at EBI and has proven its usefulness. Considering all mentioned above we believe the ontoCAT R package can be extermly useful for the bioinformatics society working in the R environment. The package is based on the Ontology Common API Tasks Java library (http://www.ontocat.org). We are providing two versions of the ontoCAT R package: - Light ontoCAT package version is available in Bioconductor starting from the release 2.7. It includes all functionality except methods to work with batch of ontologies, since Bioconductor package size is limited with 2 MB. - Full ontoCAT package version includes batch methods and is available from the ontoCAT website http://www.ontocat.org/wiki/r