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By emulating the behaviour of the OWL2 hasKey construct we have shown the potential for false positives in defining two instances as identical. For instance, BioPAX has multiple types of cross-references. These include unificationXref (for cross-references linking to semantically identical entries in the other data resources) and relationshipXref, which implies a less rigorous link. If the wrong type of key is created, or an imprecise rule is used, then two instances could be incorrectly marked as identical (via the owl:sameAs construct). This could lead to false positives with respect to related, but not identical, instances.
Another source of false positives is the large number of interactions available relating directly to the gene or protein of interest.