Identification of Equivalent Instances

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.

Figure 14: SQWRL Rule TUO_SQWRL_00003. TUO_SQWRL_00002 (not shown here) is a version of TUO_SQWRL_00003, but with UniProt as the database name rather than SGD.
\begin{figure}$tuo:Protein(?someEntity)$ $\wedge$ \\
$tuo:hasDatabaseReferenc...
...002625'')$ $\rightarrow$ \\
$sqwrl:selectDistinct(?someEntity)$\end{figure}

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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