Other than the rules described for the syntactic ontologies, some telomere ontology-specific rules needed to be created to aid querying.
The first two (TUO_00001 in Figure 12, and TUO_00002 in Figure 13) assign instances containing particular names or synonyms to the Rad9 class.
These two SWRL rules add the following instances to Rad9:
cpath:CPATH-92332 upkb:protein_0
These two instances can then be declared equivalent through the use of the owl:sameAs construct.