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[protege-owl] Variations in owl output of actual identical ontologies

Christian Knuepfer tral at
Mon Aug 6 01:55:39 PDT 2007


Some days ago I sent already a question to this list, but unfortunately 
there was no answer. So I'll try to ask a little bit different...

I create a little owl file *) with Protege 3.2.1 (test.1.owl). After 
restarting Protege and loading the file I just wrote it back (test.owl). 
Nothing was changed, no settings were altered. Now look at the 
differences between this two files:

 ~/tmp/test > diff test.owl test.1.owl
<     <rdfs:seeAlso>
<       <owl:Thing rdf:ID="Thing_2"/>
<     </rdfs:seeAlso>
<     <rdfs:isDefinedBy rdf:resource="#Thing_2"/>
 >     <rdfs:isDefinedBy>
 >       <owl:Thing rdf:ID="Thing_2"/>
 >     </rdfs:isDefinedBy>
 >     <rdfs:seeAlso rdf:resource="#Thing_2"/>

I found this result quite annoying! Such a big diff between two 
(semantically) identical "ontologies". Indeed this behaviour of the 
Protege owl export makes revision control of ontologies almost impossible!

What do you think about this. Maybe there were already discussions on 
this topic on this list, but I couldn't find them...



*) Don't worry about the content it's just to illustrate the point.

Christian Knuepfer
Friedrich-Schiller-Universitaet Jena
Institut fuer Informatik
Ernst-Abbe-Platz 1-4
D-07743 Jena, Germany

currently at:
EMBL-EBI, Wellcome-Trust Genome Campus
Hinxton, Cambridge
CB10 1SD, UK

Mobile: Intl.+44-(0)7942-333513

e-mail: tral at

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