Abstract:

Bioinformatics manages the information that has been gathered in databases since the advent of the molecular biology technological revolution. With the recent advance in bio-technology and bioinformatics, numerous genome databases from various biological communities have been developed to assist in genomic research. There are hundreds of genomic and biological databases open for common access throughout the World Wide Web. When using more than one data store or analysis tool, a biologist needs to be sure that the knowledge within one resource can be reliably compared to those in another. Information integration in general and in biology in particular requires a consistent shared understanding of the meaning of that information. 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, bio-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. Thus, bio-ontologies provide a shared and common structure of a domain thus giving a common understanding of this domain, and may be used for overcoming semantic heterogeneity. 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. However, for bio-ontologies there are also the same problems that exist for ontologies in general, namely the creation of ontology development tools (editors), development of methodologies supporting the development and use of ontologies. In this article, we review the current position in bio-ontologies and what benefits it might bring to ontologies and their use within biomedicine.

Keywords:

ontologies, bio-ontologies, knowledge representation, open biomedical ontologies, gene ontology.