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This article is part of the supplement: Semantic Web Applications and Tools for Life Sciences, 2008

Open Access Research

OGO: an ontological approach for integrating knowledge about orthology

Jose Antonio Miñarro-Gimenez1, Marisa Madrid2 and Jesualdo Tomas Fernandez-Breis1*

Author Affiliations

1 Departamento de Informática y Sistemas, Universidad de Murcia, Murcia, 30100, Spain

2 Cell Division Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, M204BX, UK

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BMC Bioinformatics 2009, 10(Suppl 10):S13  doi:10.1186/1471-2105-10-S10-S13

Published: 1 October 2009

Abstract

Background

There exist several information resources about orthology of genes and proteins, and there are also systems for querying those resources in an integrated way. However, caveats with current approaches include lack of integration, since results are shown sequentially by resource, meaning that there is redundant information and the users are required to combine the results obtained manually.

Results

In this paper we have applied the Ontological Gene Orthology approach, which makes use of a domain ontology to integrate the information output from selected orthology resources. The integrated information is stored in a knowledge base, which can be queried through semantic languages. A friendly user interface has been developed to facilitate the search; consequently, users do not need to have knowledge on ontologies or ontological languages to obtain the relevant information.

Conclusion

The development and application of our approach allows users to retrieve integrated results when querying orthology information, providing a gene product-oriented output instead of a traditional information resource-oriented one. Besides this benefit for users, it also allows a better exploitation and management of orthology information and knowledge.