No need to create a canonical representation and then to check it. There 
are at least two tools to help you with:

1) rdf-utils allow you to check for diffs in the RDF graph.

<http://wymiwyg.org/2005/12/22/announicing-rdf-utils?appendLang=en>

2) KAON2 OWL tools allow you to check for diffs in the OWL ontology that 
is represented by the RDF graph.

<http://owltools.ontoware.org>

Both should work out of the box. The latter maybe offers a bit of a 
higher abstraction, but it fails if both ontologies are not within OWL 
DL. I didn't try out the former, but as far as I understand the 
description it should work fine on the triple level, which is probably 
what you need here.

I think neither works on the model, but both work on the RDF structure, 
which may or may not be what you want. I am not sure if there is a 
model-aware version of such a tool. I should write one :)

I hope this helps,
denny

Rzepa, Henry wrote:
> Assuming we can extract RDF from our SMW, we would like to compare it
> logically with some  "hand crafted" RDF produced for what we assume is
> the same collection of facts.
> 
> What is the best way of comparing two sets of such facts to isolate
> discrepancies.  Does the concept of canonicalised  RDF exist? 

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