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[protege-discussion] Source Control Mightmare

Thomas Russ tar at ISI.EDU
Tue Jan 30 09:58:41 PST 2007

On Jan 30, 2007, at 9:45 AM, Samson Tu wrote:

> Have you tried to do the version comparison and merging using the  
> Prompt
> plugin that comes with Protege? That's what the plugin is designed  
> to do.

That certainly helps with the merging step, but it doesn't solve
the problem of a real impedance mismatch between the somewhat
random order terms are saved by Protege and the assumption of
small, incremental and local changes that is made by source control
systems like CVS or SVN.

Defining a canonical order in which to save information would
greatly aid in using such source control tools with Protege
ontologies.  This would be a big help for large projects, so
I need to express my support for John's feature request.

It wouldn't really be all that hard to do, either.  All that
is required is to decide on the order to save (i.e., Classes
or Properties/Slots first) and then sort the objects by their
name before saving.  I have done this for an export plugin I
wrote and it isn't all that difficult.  An additional sort
on template slot information for classes will also cause the
substructure to be sorted.

That would at least cause the terms to appear in the same
order when there are no changes and that would go a long
way to making the resulting files work well with source
control tools.

If there is concern about the cost of sorting the objects
each time one saves, then this could be addressed by introducing
a configuration property that determines if one wants sorted
output or not.  My feeling is that sorting doesn't add much
overhead on saving, but I haven't used this on very large

But I think this would be a good feature to include in the
next version of Protege.

> John Patrick wrote:
>> Greetings,
>> I've searched the message archives but have been unable to find
>> similar problems. I've been using Protege for the last 6 months and
>> have slow started to have more and more issues with how Protege saves
>> owl files.
>> The project I'm on is maintained in a perforce repository and  
>> branched
>> as required, once a branch is finished or stable it is merged back
>> into the main branch. The issue comes when you try to merge owl  
>> files.
>> A merge is takes about 3 days, of which over 2.5 days is just sorting
>> out manually merging the owl files. Identifying changes which have
>> occurred in both branches and then implementing those changes.
>> Is there a way of getting Protege to group and sort
>> objects/properties/attributes when it saves and owl file. I don't  
>> mind
>> how its ordered or grouped I'd just like some conformity to how it
>> does it.
>> John Patrick
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> -- 
> Samson Tu                    email: swt at
> Senior Research Scientist    web:
> Stanford Medical Informatics phone: 1-650-725-3391
> Stanford University          fax: 1-650-725-7944
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