How to define hierarchical mapping for a flat data structure based upon a number of set values in columns

Let's say that I have such data as is attached on the screenshot. I want to define hierarchical mapping based upon the limited number of values present in ProtocolName and ColumnName columns but not based upon the ProtocolName and ColumnName keys that will be in the final json. Is it possible to do or transforming such flat data structure into the hierarchical one (when keys would be the actual values of ProtocolName and ColumnName) is required in Flexmonster? We have very large flat data input and if we need to transform it, it would require looping through the data and preparing the right format for Flexmonster which may take a lot of time.
The ultimate goal is just to have this flat data fed into Flexmonster and specify a number of groupby columns (on the screenshot it would be Cell Line) and see the results. We want to have rows as CompoundID and columns as, for instance, ADME Assay/EC50/L1 - val, ADME Assay/EC50/L2 - val, ADME Assay/EMax/L1 - val, ...