Modular decompositions of protein interaction networks can be used to identify modules of cooperating proteins. The biological plausibility off these modules might be questioned though. This report describes how a modular decomposition can be completed with semantic information in the visual representation. Possible methods for creating modules of functionally related proteins are also proposed in this work. The results show that such modules, with advantage can be combined with modules from a graph decomposition, to find proteins that are likely to cooperate to perform certain functions in organisms