Controlling annotation redundancy based on protein topology. (A) Schematic overview of the procedure adopted for retaining a given protein only in those FN that satisfactorily overlap (as assessed by the PMS) the topological structures to which the protein belongs. In the example shown in (B), the protein doubly annotated with the blue and green terms is initially included into the two relevant FN (rounded rectangles with dashed lines). Subsequently, however, the protein is retained in the blue node (but excluded from the green node), because (compared with the green node) the blue node overlaps better the 3-protein clique (i.e., the triangle), to which the protein belongs. As a result, in the final PG, no edge is established between the green and red nodes. In (C), the example of the Cta1p catalase is shown, while (D) shows the procedure of enucleating a function from a FN, which then undergoes relabeling. See also Additional file 3 for the distribution of FN and edges at different NTS.