Bio-Ontologies: A Knowledge Representation Resource in Bioinformatics

Bioinformatics manages the information that has been gathered in databases since the advent of the molecular biology technological revolution. The successful research is based in interpretations of that information that can be accessed and managed computationally, which is a difficult task. An attempt to solve that problem is to use ontologies. Ontologies are computational formalisations of the knowledge about a given domain, allowing computers to manage the information in a semantic level. In medical informatics, ontologies have been used for a longer period of time to produce controlled lexicons for coding schemes. Bio-ontologies define the basic terms and relations in biological domains and are being used among others, as community reference, as the basis for interoperability between systems, and for search, integration and exchange of biological data. The most successful ontologies applied in Bioinformatics are the ones in the Open Biomedical Ontologies (OBO) project. At the same time, the Web Ontology Language (OWL) is a official proposal for ontologies implementation in the semantic web. In this article, we review the current position in bio-ontologies. We review this trend and what benefits it might bring to ontologies and their use within biomedicine.