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Open Access Technical Note

OntoFox: web-based support for ontology reuse

Zuoshuang Xiang123, Mélanie Courtot4, Ryan R Brinkman45, Alan Ruttenberg6 and Yongqun He123*

Author Affiliations

1 Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA

2 Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA

3 Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA

4 Terry Fox Laboratory, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada

5 Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada

6 Science Commons, 77 Massachusetts Avenue Room E25-131, Cambridge MA 02139, USA

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BMC Research Notes 2010, 3:175  doi:10.1186/1756-0500-3-175

Published: 22 June 2010

Abstract

Background

Ontology development is a rapidly growing area of research, especially in the life sciences domain. To promote collaboration and interoperability between different projects, the OBO Foundry principles require that these ontologies be open and non-redundant, avoiding duplication of terms through the re-use of existing resources. As current options to do so present various difficulties, a new approach, MIREOT, allows specifying import of single terms. Initial implementations allow for controlled import of selected annotations and certain classes of related terms.

Findings

OntoFox http://ontofox.hegroup.org/ webcite is a web-based system that allows users to input terms, fetch selected properties, annotations, and certain classes of related terms from the source ontologies and save the results using the RDF/XML serialization of the Web Ontology Language (OWL). Compared to an initial implementation of MIREOT, OntoFox allows additional and more easily configurable options for selecting and rewriting annotation properties, and for inclusion of all or a computed subset of terms between low and top level terms. Additional methods for including related classes include a SPARQL-based ontology term retrieval algorithm that extracts terms related to a given set of signature terms and an option to extract the hierarchy rooted at a specified ontology term. OntoFox's output can be directly imported into a developer's ontology. OntoFox currently supports term retrieval from a selection of 15 ontologies accessible via SPARQL endpoints and allows users to extend this by specifying additional endpoints. An OntoFox application in the development of the Vaccine Ontology (VO) is demonstrated.

Conclusions

OntoFox provides a timely publicly available service, providing different options for users to collect terms from external ontologies, making them available for reuse by import into client OWL ontologies.