Fig. 2

Instance-based semantic graphs of parthood relations with a corresponding SPARQL Query. a Left: shows the parthood named graph instance associated with the anatomical entity that is at the root of the partonomy. It is an instance of the ontology class ‘parthood named graph’ and contains the URI of the root entity (i.e., the entity that is being described) together with its class affiliation and its human readable label. a Right: shows the parthood named graph instance associated with some parts of the root entity. It is also an instance of the class ‘parthood named graph’, but contains, in addition to its own URI, class affiliation and human readable label, also the URI of its direct parent entity and the parthood relation between them. The union of all instances of ‘parthood named graph’ of a given Semantic Instance Anatomy documents the direct parthood relations of all described parts together with their class affiliation and their human readable label. For reasons of clarity, resources are not represented with their URIs but with labels. 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 three-step SPARQL Query that makes a union of all parthood named graphs of a given document. The first query searches for the URI of the instance of ‘assertions named graph’ in the ‘document named graph’. The second query searches for the instance of ‘instance anatomy’ within this assertions named graph. The sub-query of the third query searches within this assertions named graph for all triple statements that have Subject: ‘instance anatomy’ and Predicate: ‘bfo:has part’ and retrieves a list of named graph resources. The result of this sub-query is filtered for individual named graph resources of the type ‘parthood named graph’. The main query provides the union data of the filtered named graphs from the sub-query (the result of this query is documented in Additional file 2)