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OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript

Tomasz Adamusiak1*, Tony Burdett1, Natalja Kurbatova1, K Joeri van der Velde2, Niran Abeygunawardena1, Despoina Antonakaki2, Misha Kapushesky1, Helen Parkinson1 and Morris A Swertz12

Author Affiliations

1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK

2 Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and Groningen Bioinformatics Center, University of Groningen, P.O. Box 30001, 9700 RB, Groningen, The Netherlands

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BMC Bioinformatics 2011, 12:218  doi:10.1186/1471-2105-12-218

Published: 29 May 2011



Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups.


OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application.


OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases.

Availability webcite