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[protege-owl] Unique cannonical serialization (using Subversion or some such)

Alan Ruttenberg alanruttenberg at
Tue Mar 17 14:59:05 PDT 2009

Hi Tanya,
While I agree with the general sentiment, I don't agree that text diffs
won't be useful. In fact in many cases they will be. I think that by
default, protege should try as hard as it can to have a stable rendering of
the ontology, and this isn't *that* hard to do. There isn't any good reason,
as far as I can tell, for the current situation, in which even ontologies
that are not changed at all are serialized in a different order each time.

Regarding the prompt plugin, I just tried it and was put off by the fact
that I couldn't point it at an OWL file - it only takes pprjs and I didn't
have one for our previous release.

I'm aware of the experimental serialization method. It's a reasonable start.
If it's past being experimental, then I suggest removing the label and
making it the default serialization. If it is still experimental, then it
would be good to know how much it can be trusted currently and when it can
be expected to be stable enough to use for 'production'.

Past that, what would be very helpful would be for the NCBO to put out a
command line tool OWL diff tool that can be configured for uses with svn
(via --diff-cmd) and instructions for how to set it up. There is a
significant clientel for tools that play nice on the command line.


On Tue, Mar 17, 2009 at 2:54 PM, Tania Tudorache <tudorache at>wrote:

> Hi Eric,
> I don't think it is a good idea relying on a particular serialization,
> but I understand your set up. Protege 3.x IS using Jena to write out the
> OWL file, that is why it is different each time, so writing your own
> serialization using Jena won't help :)
> Instead, you can use the native writer which you can configure from OWL
> menu -> Preferences -> Experimental native writer. If you will also
> enable the 'Sort resources alphabetically' checkbox, then the output
> will be repeatable across different Protege work sessions.
> There have been several emails on the list about using OWL files stored
> in SVN. You should be able to find them in the archive. Main problem is
> that a text-based diff of an RDF serialization of OWL will not be
> useful, as the same OWL axiom can be expressed and serialized in
> different ways (e.g. rdfs:subclass of A -> B, B-> A; and A
> owl:equivalentClass B, etc.)
> So, a text diff will not give the users what they want. There are
> several structural diff tools that you could use that will give a much
> better result. PromptDiff is one of them, is already integrated in
> Protege, and is also used in another project in a production setting.
> So, a combination of SVN with PromptDiff (or another OWL diff tool)
> would work.
> There are other alternatives:
> 1. Rather than using Protege 3.x, you should use Protege 4 which uses
> the OWL-API and has a much nicer and user-friendly serialization of OWL.
> It also has support for OWL 2 features that Protege 3.x does not. It
> also supports the rendering of an OWL ontology in different formats that
> might be more "SVN friendly".
> 2. Protege 3.x already has support for collaborative ontology
> development that is integrated in the tool. You can take a look at
> Collaborative Protege [1]
> 3. There is a web-based repository tool that might be interesting that
> works with protege as a backend for OWL and RDF.  It keeps track of
> changes, dumps them as RDF files, and has many other nice features
> (visualization, annotation, search, etc.). The tool is open source and
> is domain-independent. You can see an example of the tool here,
> BioPortal [2].
> Tania
> [1]:
> [2]:
> Eric Peterson wrote:
> >
> > Hi folks;  (I misposted this as a followup)
> >
> > I'm having a hard time collaborating Protege-wise with my cohorts.  We
> > are a Subversion shop, but due to the fact the Protege serializes
> > vastly differently for small changes, we can't diff and merge
> > conflicting versions of our OWL files.
> >
> > I don't think I could sell the use of Protege's collaboration tools,
> > but would value suggestions for solving this problem.
> >
> > I'm considering writing my own serialization plugin for Protege using
> > Jena.
> >
> > Thanks!
> >
> > -Eric Peterson
> >
> >
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