This is a better picture of what the dependencies were like in bioclipse:
The dashed lines indicate some kind of vague boundary between plugin 'layers'. There's no such concept of a plugin layer, as far as I know, but still. Of course, there is the net.bioclipse.core plugin, which could be considered to be an inner core.
It may be an artificial distinction to make between the 'data' and 'analysis' layers, but basically the data plugins do the open-edit-save cycle mentioned here while the analysis plugins do more. Specifically, the seneca and medea plugins can produce spectra data from molecule data.