GeoKnow deliverable 2.7.1 describes set of XSLTs for INSPIRE to RDF, which are also available.
XSLTs do a basic job, transformation is basic and only uses/converts what is in the INSPIRE data
i.e. doesn't really use the Linked part of Linked Data (not a criticism, just a practical reality)
http://geodata.gov.gr/sparql/ is online but seems to have a problem, can't get hold of owners.
So working entirely from what the XSLT tells me.
We should use the URIs defined in the INSPIRE Registry. See, for example, Natura2000 Designations. That takes care of the designation scheme and designation, but not the percentage under designation.