Formalization of gene ontology relationships with factor graph towards biological process prediction

Abstract

Gene Ontology is a hierarchical controlled vocabulary for protein annotation. Its synergy with automatic classification methods, ensemble, has been widely used for the prediction of protein functions. Current classification methods use only the relation is a and a few little part of to generate prediction model. In this work we formalize the GO part of, regulates; negatively regulates and positively regulates relationships through predicate logic. This formalization is incorporated within an ensemble method based on graph factor called Factor Graph GO Annotation. The proposed model is validated against four model organisms for GO Biological Process prediction.