Natural science is where the objective and the subjective meet. When we build data collections, we want them to reflect the objective relations inherent in nature, but also classify these collections, adding subjective relations between data objects. Sometimes these two approaches conflict. We present two examples of blending objective and subjective relations in a single data collection, and discuss some possible generalizations. First example deals with the visualization of metabolic networks in three dimensions. We show that the network topology has a substantial subjective component in this case and discuss possible ways to minimize human inference. In the second example we present a collection of metabolic networks as a (subjective) hierarchical structure with (objective) binary relations between objects, and show how the data visualization may be made more logical via the procedure of "hierarchization of relations".