Figure out why some phyloreferences don't resolve correctly in JFact

[gaurav]

I accidentally ran the Clade Ontology using the JFact reasoner instead of the FaCT++ reasoner today, which lead to the discovery that some phyloreferences that resolve correctly in the latter don't resolve in the former. I couldn't find any obvious pattern in which ones resolved and which didn't. This isn't important yet, but might be worth digging into at some point.