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[protege-discussion] Protege db schema conversion

Todd Detwiler det at u.washington.edu
Mon Dec 3 15:04:14 PST 2012


Please see my answers to follow-up questions below.
Thanks,
Todd

Landon Todd Detwiler
Structural Informatics Group (SIG)
University of Washington

phone: 206-616-2336

On 12/3/12 2:22 PM, protege-discussion-request at lists.stanford.edu wrote:
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 03 Dec 2012 12:37:36 -0800
> From: Timothy Redmond <tredmond at stanford.edu>
> To: protege-discussion at lists.stanford.edu
> Subject: Re: [protege-discussion] Protege db schema conversion
> Message-ID: <50BD0D90.5030501 at stanford.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> My first reaction was that I am not sure what is wrong but perhaps
> getting some clarification on parts of the message will help me figure
> out what is wrong.
>
> On 11/28/12 3:17 PM, Todd Detwiler wrote:
>> Through the life of Protege as a tool, the database schema has
>> undergone a few changes. As far as I know, the best approach for
>> upconverting the schema of a database ontology has always been to
>> first export it to clips (in an older Protege version) and then open
>> that clips file in a newer Protege version and then save it out to a
>> db. This has worked for us reasonably well in the past (we have an
>> ontology for which the developers still use an old Protege version).
>> But lately this isn't working well any more. I can still successfully
>> write out our ontology to clips files. Newer versions of Protege (i.e.
>> 3.4.7, 3.4.8, and 3.5beta) can open the clips file and things look OK.
> This makes it sound like you have successfully converted the database
> project to a clips project.  I am also assuming from this description
> that you are using Protege frames and not Protege OWL.

It appears so. I have converted the project to clips and, superficially, 
it looks fine in Protege. This is a fairly large ontology (the FMA) at 
80,000+classes and over 2 million relationships. So, it does take a 
while to convert to clips and a rather large heap. Oh, and yes it is in 
frames.

>
>> But when I try and save it out to a db, things go wrong. The resultant
>> db, in the Protege UI, looks like all of our classes are untyped
>> (nothing in the right hand pane).
> It sounds like you have taken a valid clips backed Protege frames
> project, converted it to a Protege Database project (not a OWL/RDF
> Database) project.  After doing the conversion, it sounds like the
> database project does not look the same as the clips backed project.  If
> so, it sounds like this is where the problem occurred. Did you use one
> of the supported datablases (mysql or postgres)?  Is it possible to send
> us the ontology so that we can try it out?

Yes, I have loaded the clips project (in multiple Protege versions) and 
attempted to "Convert project to format" frames database. But it does 
not look the same in Protege (as the clips version). None of the classes 
have any info in the right frame (as though they were un-typed). Also, 
many leaf concepts don't appear at all (in the tree). I can query the 
database and find the missing classes. And, they have valid types. I am 
using MySQL for my database backend. In fact, I am using the same 
instance of MySQL that the initial db was in (before upconverting the 
schema). I can send you the file, but it is too large for email, even 
when compressed. So I've uploaded it here: 
http://dl.dropbox.com/u/2527438/FMA3.3/fma_3_3.sql.zip
>
>> Also, lots of leaf classes appear to be missing in the tree. Now, if I
>> query the database, these classes exist and have types.
> Are you talking about sql queries here?

Yes, SQL queries.

>
>> Further, if I open the new database ontology in Protege 3.4beta, it
>> looks fine.
> So the new database project looks fine in one version of Protege
> (3.4.*?) but not in another one (3.5?)?  I believe that the database
> backend format should be identical between the later 3.4 versions and
> the 3.5 version.

That is correct. It does not look fine in 3.4.7, 3.4.8, or 3.5beta. But 
it does display fine in 3.4beta.

Thank you for any help you can offer,
Todd

>
> -Timothy
>
>> What changes have occurred in the database backend, since 3.4beta,
>> that could be causing this?
>> Thanks,
>> Todd
>>
>
>
>



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