%0 Journal Article
%T Defining functional distances over Gene Ontology
%A Angela del Pozo
%A Florencio Pazos
%A Alfonso Valencia
%J BMC Bioinformatics
%D 2008
%I BioMed Central
%R 10.1186/1471-2105-9-50
%X We propose a new method to derive 'functional distances' between GO terms that is based on the simultaneous occurrence of terms in the same set of Interpro entries, instead of relying on the structure of the GO. The coincidence of GO terms reveals natural biological links between the GO functions and defines a distance model Df which fulfils the properties of a Metric Space. The distances obtained in this way can be represented as a hierarchical 'Functional Tree'.The method proposed provides a new definition of distance that enables the similarity between GO terms to be quantified. Additionally, the 'Functional Tree' defines groups with biological meaning enhancing its utility for protein function comparison and prediction. Finally, this approach could be for function-based protein searches in databases, and for analysing the gene clusters produced by DNA array experiments.Current genome sequencing projects are producing a wealth of data in the form of sequences of biological polymers. For this data to be useful, it has to be interpreted in functional terms. Thus, efficient systems to describe and classify protein function are needed, as well as tools to predict the function of the huge number of new sequences.There is much evidence for the need of well-defined and structured functional descriptions [1-4]. However, the main difficulty encountered is that 'function' is not a well defined concept and it is not as un-equivocal as 'sequence' or 'structure'. Indeed, protein function is a very complex and multidimensional phenomenon.In many cases, functional descriptors are based on the available experimental techniques or are due to historical reasons. However, they do not necessarily have any meaning in biological terms (evolution, molecular mechanism). The methods we use to study biological systems require conceptualization and categorization, which are sometimes taken beyond their role as mere tools of the scientific method and are 'imposed' on the cell. One example i
%U http://www.biomedcentral.com/1471-2105/9/50