Fig. 1.

Instance-based semantic graph of a document and its parts with a corresponding SPARQL Query. a An instance-based semantic graph representing the structure of a document, stored in a named graph instance of the ontology class ‘document named graph’. The graph relates an instance of the IAO class ‘document’ to instances of other IAO classes, all of which refer to different parts of a typical scientific publication. Some of these parts may themselves have parts, which are modeled as a semantic graph (here not shown), whereas others only have a literal value associated. Purple-bordered box = ontology individual; purple-bordered grey box = named graph instance; yellow-bordered box with rounded corners = ontology class; grey-bordered box = literal or numerical value; arrow = property. b A two-step SPARQL Query to access the named graph shown in A. The first query searches for the URI of the named graph. We know the URI of the entry, which is the instance of the IAO class ‘document’, and we know that the document named graph contains the triple statement Subject: ‘document’, Predicate: ‘rdf:type’, Object: ‘iao:document’. We thus search for the named graph that contains this triple statement. In the second query we retrieve all triple statements contained in this named graph (the result of the second query is documented in Additional file 1)