The next step is to discover equivalent instances elsewhere in the integrated schema and mark them as such. We do this by mimicing the behaviour of the OWL2 construct owl:hasKey (see http://www.w3.org/TR/owl2-syntax/#Keys). The end result of this procedure is that all instances with the same SGD accession will be marked as identical using the owl:sameAs construct. In future, this will happen automatically as the relation linking a telomere ontology Protein to its SGD accession number will be classed as the key for the Protein class in an owl:hasKey construct.
Until the owl:hasKey construct is available, those instances having the same SGD accession are identified using the SQWRL query described in Figure 14, and then manually adding the owl:sameAs assertions. We use a SQWRL query rather than a SWRL rule here, as SWRL rules modify the target ontology.
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There are already two instances of Rad9 as a result of the rules described in Figure 12 and Figure 13. After running the query in Figure 14 and viewing the results (upkb:protein_0 and psimif:interactor_59), the owl:sameAs construct can be applied between those two instances. The new instance, psimif:interactor_59, does not contain `rad9' in its name or synonyms, but does contain a matching SGD accession.
After inferring the placement of all individuals in the ontology using a reasoner, psimif:interactor_59 is inferred as an instance of Rad9, bringing the total number of Rad9 instances to three:
cpath:CPATH-92332 upkb:protein_0 psimif:interactor_59
As all of these instances are marked as equivalent, the knowledge contained within each of them is accessible as a single logical unit.
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