I've been talking with DavidBooth regarding virtual graphs support. A summary of my current position follows:
I woke up today feeling like I have a decision on this. It seems that you have a concern with regard to data in the user space causing accidental merging of graphs within virtual graphs which are then accidentally queried. On the other hand, I have the concerns that (a) there is an added cost to the step resolving a virtual graph to its component graphs; and (b) without introducing a new index, we have no place outside of the "user data" to store those virtual graph => component graph associations.
Given both of our concerns, I think that it makes sense to do something like Anzo using an explicit syntax to address the virtual graphs and using a bigdata specific predicate to create those associations.
I believe the Anzo syntax is:
FROM NAMED DATASET
Or we could use
FROM VIRTUAL GRAPH
FROM NAMED VIRTUAL GRAPH
Personally, I prefer the latter as it more directly conveys the concept.
In terms of modeling the virtual graph relationships:
:vg bd:virtualGraph :vgx
Would establish a membership relationship indicating that :vgx is a member of the virtual graph :vg. The bd: namespace would be the namespace for bigdata specific extensions.
As far as I can see, there is no distinction when modeling virtual graph membership between named graphs and the default graph. That is simply a question of whether you reference the virtual graph in the FROM VIRTUAL GRAPH or FROM NAMED VIRTUAL GRAPH clause of the query.
When a graph identifier is encountered in FROM (NAMED) VIRTUAL GRAPH clause it will be resolved to the member graphs and the data set will be rewritten to use the member graphs instead of the specified graphs.
I am agnostic as to where those bd:virtualGraph assertions should live. I presume that we will use the SPOC index to locate them. In that case, the assertions will be clustered in the index and can be quickly resolved whether they are in the same graph or different graphs.
I do not believe the presence of the bd:virtualGraph assertions will cause troubles with user data due to the open world nature of RDF and the combination of the bigdata specific assertion and the deliberate use of a syntactic means to indicate that the virtual graph is to be addressed.
I have added a wiki page to document this feature .
 https://sourceforge.net/apps/mediawiki/bigdata/index.php?title=VirtualGraphs&action=submit (Virtual Graphs wiki page)