Based on the stoichiometric structure of conservational processes, a general methodology has been developed for the computer aided generation and operation of network interoperability services. An appropriate set of unified building elements, having autonomous programs and communicating with a dynamic simulating kernel has been elaborated for the qualitative and quantitative tracing and tracking of trans-sectorial processes. The GNU-Prolog implemented method is scalable and makes possible the ad hoc extension of the models with the actually interesting components to be investigated. The system can also be applied for the identification of hidden resources and wastes, as well as for the analysis of the value chains. This outlines a straightforward cooperative architecture of services between the planned interoperability center and the actors, supervised by the responsible authorities. The method will be illustrated by the example of agrifood processes.