While examining the code today, I noticed that there were both ‘data’ and ‘data2’ prefixes in swo_core.owl and swo_data.owl. For some reason, both swo_core and swo_data had incorrect ontology prefixes ‘data’ and ‘data2’ set to “http://www.ebi.ac.uk/swo/data/http://www.ebi.ac.uk/swo/data/”, which is a weird duplication of the correct URL. All instances of this incorrect prefix were removed from both files. swo_data remains consistent via HerMIT reasoner from within Protege 4. This fix was committed at revision 256 of the sourceforge SVN respository.