Gene Ontology (GO), the de facto standard for representing protein functional aspects, is being used beyond the primary goal for which it is designed: protein functional annotation. It is increasingly used to evaluate large sets of relationships between proteins, e.g. protein-protein interactions or mRNA co-expression, under the assumption that related proteins tend to have the same or similar GO terms. Nevertheless, this assumption only holds for terms representing functional groups with biological significance (classes), and not for the ones representing human-imposed aggregations or conceptualizations lacking a biological rationale (categories).