Is there a hierarchy within Pfam domains or with other methods in InterPro?
Pfam itself does not have a hierarchy since no 2 Pfam HMMs should ever overlap on a sequence, unless one is a nested domain. However, there may be a Prints or other signature which defines a subset/subfamily of a Pfam family. In InterPro we found many such cases so we have a hierarchy of parent/child relationships. We also have a contains/found in relationship which is used when a domain is found in a family of proteins. In this way there is some sort of hierarchy of Pfam in relation to other signature database signatures.