OMG! How many PhD students really behind the “Ioan_Filip” moniker? Like 10? 
This is the work of a whole department. You are truly ambitious. Well, good luck with your studies.
All of these use cases are very useful and interesting, and the OMOP/OHDSI system will allow you to study them. Well, the phenotype aspect, that is. We currently don’t have any real support for omics, even though that bubbles up as a future direction all the time, When you talk about point clouds and clustering procedures - are you talking about geographical distribution of effects? There are folks work on this already. You may want to hook up.