This article is part of the supplement: Proceedings of the 11th Annual Bioinformatics Open Source Conference (BOSC) 2010

Open Access Proceedings

ONTO-ToolKit: enabling bio-ontology engineering via Galaxy

Erick Antezana1*, Aravind Venkatesan1, Chris Mungall2, Vladimir Mironov1 and Martin Kuiper1

Author affiliations

1 Department of Biology, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, N-7491 Trondheim, Norway

2 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA

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Citation and License

BMC Bioinformatics 2010, 11(Suppl 12):S8  doi:10.1186/1471-2105-11-S12-S8

Published: 21 December 2010



The biosciences increasingly face the challenge of integrating a wide variety of available data, information and knowledge in order to gain an understanding of biological systems. Data integration is supported by a diverse series of tools, but the lack of a consistent terminology to label these data still presents significant hurdles. As a consequence, much of the available biological data remains disconnected or worse: becomes misconnected. The need to address this terminology problem has spawned the building of a large number of bio-ontologies. OBOF, RDF and OWL are among the most used ontology formats to capture terms and relationships in the Life Sciences, opening the potential to use the Semantic Web to support data integration and further exploitation of integrated resources via automated retrieval and reasoning procedures.


We extended the Perl suite ONTO-PERL and functionally integrated it into the Galaxy platform. The resulting ONTO-ToolKit supports the analysis and handling of OBO-formatted ontologies via the Galaxy interface, and we demonstrated its functionality in different use cases that illustrate the flexibility to obtain sets of ontology terms that match specific search criteria.


ONTO-ToolKit is available as a tool suite for Galaxy. Galaxy not only provides a user friendly interface allowing the interested biologist to manipulate OBO ontologies, it also opens up the possibility to perform further biological (and ontological) analyses by using other tools available within the Galaxy environment. Moreover, it provides tools to translate OBO-formatted ontologies into Semantic Web formats such as RDF and OWL.


ONTO-ToolKit reaches out to researchers in the biosciences, by providing a user-friendly way to analyse and manipulate ontologies. This type of functionality will become increasingly important given the wealth of information that is becoming available based on ontologies.