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The need to manage the complexity of current systems encourages the use of models in Engineering processes. Systems Engineering is a multi-domain discipline which implies a wide variety of heterogeneous design models in the life-cycle of the system. Furthermore, dividing of the work and the advent of collaborative engineering techniques require combination of these heterogeneous models in order to achieve the overall engineering process. In such a context, we propose a methodology making possible to interoperate existing heterogeneous design models. Our approach fastens upon knowledge in order to annotate and homogenize the models. More precisely, we claim that design models can be completed or clarified with shared domain knowledge, i.e. ontologies, which is mastered by the engineers but usually not formalized. Moreover, this methodology is not intrusive since it aims to link models by developing an additional model of relations which allows keeping the traceability to the original models.