Hi Nic,
Thanks for your post.
I think the most important point to make is that although we are using Protege, we are not using OWL. For some more background into why, have a look at
this blog article I wrote about OWL. Please note, this is not a critique of OWL per se, rather an answer to the FAQ of why we have chosen not to use OWL.
We have purposely chosen to work with Protege Frames, which enables us to very clearly separate the development of the meta model from the capture of instances. As you populate the model, we are creating an ontology about your enterprise. Reasoning in various forms is at the heart of how the Essential platform works - typically delivered by the Views - and the meta model has grown over time to provide very clear semantics for the model/ontology.
Depending on your philosophy to the purpose of the model that you build in Protege, your choice of OWL or Frames might be more appropriate.
In terms of the Essential Architecture Manager toolset, I also think it's worth noting that this is the reference implementation of the Essential Meta Model. We have developed the meta model over the last 11 years or so and whilst we have developed all our widgets and the Essential Viewer platform of Essential Architecture Manager to work with any meta model (which is obviously very advantageous for the continuing development of that!) we can't guarantee that all the components will work as expected with an OWL project in Protege.
In terms of how Essential Architecture Manager works, have a look at the
over of Essential Architecture Manager, which gives a good overview how it works.
The Viewer environment, as I described in
a more recent blog, is really a toolkit for producing the views that you require. We provide some out of the box but we certainly don't expect this to be all you'd ever need. Rather we expect users to use the included views as a starting point from which to produce their own views - remember that each view (from a TOGAF point of view) is generated dynamically. The Essential Views are templates that are used by the Viewer to generate each particular view.
Hope this helps
Jonathan