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Open Access Software

OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology

Kieran O'Neill125, Alexander Garcia4*, Anita Schwegmann3, Rafael C Jimenez15, Dan Jacobson1 and Henning Hermjakob5

Author Affiliations

1 Central Node, National Bioinformatics Network, Golf Park, Raapenberg Road, Cape Town, South Africa

2 School of Computer Science, University of KwaZulu-Natal, King Edward Avenue, Pietermaritzburg, South Africa

3 Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa

4 Faculty of Linguistics and Literary Sciences, University of Bremen, Bremen, Germany

5 EMBL Outstation-European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK

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BMC Bioinformatics 2008, 9:437  doi:10.1186/1471-2105-9-437

Published: 16 October 2008

Abstract

Background

Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms.

Results

OntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing ontology-based queries against the Gene Ontology Database. Both a comprehensive use case and the interface itself were designed in a participatory manner by working with biologists to ensure that the interface matches the way biologists work. OntoDas was further tested with a separate group of biologists and refined based on their suggestions.

Conclusion

OntoDas provides a visual and intuitive means for constructing complex queries against the Gene Ontology. It was designed with the participation of biologists and compares favourably with similar tools. It is available at http://ontodas.nbn.ac.za webcite