Input-output (IO) models, describing trade between different sectors and regions, are widely used to study the environmental repercussions of human activities. A frequent challenge in assembling an IO model or linking several such models is the absence of flow data with the same level of detail for all components. Such problems can be addressed using proportional allocation, which is a form of algebraic transformations. In this paper, we propose a novel approach whereby the IO system is viewed as a network, the topology of which is transformed with the addition of virtual nodes so that available empirical flow data can be mapped directly to existing links, with no additional estimation required, and no impact on results. As IO systems become increasingly disaggregated, and coupled to adjacent databases and models, the adaptability of IO frameworks becomes increasingly important. We show that topological transformations also offer large advantages in terms of transparency, modularity and increasingly importantly for global IO models, efficiency. We illustrate the results in the context of trade linking, multi-scale integration and other applications.