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[protege-discussion] protege-discussion Digest, Vol 77, Issue 6

Todd Detwiler det at u.washington.edu
Fri Dec 7 10:49:22 PST 2012


Timothy,
Thank you very much for the info. Yes this is helpful. I hadn't noticed 
that all of the is_template values were set to true. Now the question 
is, is this happening when converting the clips project into a db 
project. If you have any time to look at my clips files, I have posted 
them here: 
http://dl.dropbox.com/u/2527438/FMA3.3/fma_3.3_frames_clips.zip. I must 
warn you, however, that they require a large heap to open in this format 
(I generally use 1.5G) and it takes a bit of time to open.

Even if you don't have time to investigate, I appreciate your effort and 
feedback so far. Unfortunately it still means that I have a migration 
path problem.

Thanks,
Todd

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

phone: 206-616-2336

On 12/6/12 12:03 PM, protege-discussion-request at lists.stanford.edu wrote:
> Message: 1
> Date: Thu, 06 Dec 2012 10:59:21 -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:<50C0EB09.2080000 at stanford.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>> >
>> >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  
> Ok - I am a bit confused but there may be a hint here.  The database
> dump that you sent me is bad.  The problem that it has is that all of
> the is_template values in the database are set to 'true'.  You can see
> this in the sql dump because one of the typical entries looks like this:
>
>        (':THING',6,':DIRECT-SUBCLASSES','','^A',0,do 6,'Anatomical entity',NULL)
>
>
> where the ^A represents the binary character control-A (I think that
> this is a 1 in ascii).  You can see this in the database by running an
> sql query:
>
> mysql> select * from fma where is_template=false;
> Empty set (0.00 sec)
> mysql>
>
> This is why when I load this database and read it into Protege, I don't
> see any subclass relationships.  Protege looks for :DIRECT-SUBCLASSES
> with a isTemplate value of false and the database only has entries with
> an isTemplate value of true.
>
> Now this is where I become uncertain.  Interestingly the symptoms that I
> described are similar to some of the symptoms that you described (e.g.,
> the subclass relationships are in the database in some sense but don't
> appear in Protege).  The problem with the database dump is clear enough
> but it is not clear when in the process it got corrupted.
>
> It seems like I have found a problem but not the problem that you
> originally described.  I think that you indicated that you had a valid
> clips file that lost data when converted to a database project.  If I am
> going to replicate this, it would seem that maybe I need to start with
> the clips file.
>
> What is the next step?  Does the new information help?
>
> -Timothy
>
>
>
> On 12/03/2012 03:04 PM, Todd Detwiler wrote:
>> >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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