What does this mean?
A qualified reference is a cross-reference that explains its intent. For example, X is regulator of Y is a much more qualified reference than X is associated with Y, or X see also Y. The goal therefore is to create as many meaningful links as possible between (meta)data resources to enrich the contextual knowledge about the data, balanced against the time/energy involved in making a good data model. To be more concrete, you should specify if one dataset builds on another data set, if additional datasets are needed to complete the data, or if complementary information is stored in a different dataset. In particular, the scientific links between the datasets need to be described. Furthermore, all datasets need to be properly cited (i.e., including their globally unique and persistent identifiers).