An annotation of scaffold nodes in trees or networks with e.g. bioactivity data can be achieved via the stored origin molecules as well. One way to do this is to deposit the (unique) SMILES representation of the molecules in the studied data set linked to the respective annotation in a map structure. After the hierarchy is generated, its nodes can be annotated through comparing the origin molecule SMILES codes with the previously compiled annotation map. This way, e.g. scaffold nodes could be coloured according to bioactivity or the hierarchy display limited to active scaffolds in a more advanced visualisation tool as proposed above.