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[protege-discussion] Protege 3.3.1 DB Schema

O'neill, Dennis doneill at
Thu Feb 19 05:49:20 PST 2009


We have been using the XML export to handle our ontologies so far.
However, the issue we are dealing with is that the one of the ontologies
I currently have is too large for MS SharePoint to process efficiently
as an XML import. For certain uses (SharePoint libraries), we only need
a subset, and hence want to filter the entries before XML export/import.

Having looked at the DB that is generated, I can see how it is really an
export of the Frame meta-database; but that is exactly the thing we want
to decipher. If I understood the format, perhaps I could post-process it
into a true ontology DB (tables for class instances, for example) that
we could then do our queries over.

Is there any documentation along these lines, or could you point me at
the code that does the DB creation?



Dennis M. O'Neill
Contractor to Marathon Oil Company
Enterprise Content Management
Room 2068D
(281) 236-5690 (Cell)
doneill at
-----Original Message-----
From: protege-discussion-bounces at
[mailto:protege-discussion-bounces at] On Behalf Of
Jonathan Carter
Sent: Thursday, February 19, 2009 2:47 AM
To: User support for Core Protege and the Protege-Frames editor
Subject: Re: [protege-discussion] Protege 3.3.1 DB Schema

Hi Dennis,

>From my experience of the database schema, I would advise against
operating directly (even reading) the underlying database table (note:

Protege database is basically a meta-meta-database. So, all your classes
and instances and everything are just instances of the meta-meta
classes, e.g. Frame. 
(This is roughly speaking - I haven't spent much time on the details of
this). It works really nicely but is rather complex to interpret (to say
the least) with a lot of references to other rows to follow to get the
picture that you have in Protege (the GUI editor).

When Protege sets up the database it puts some indexes in to help with
all the look ups required. (Unfortunately, there's an issue with MS
SQLServer 2005 which means that Protege 3.3.1 can't create all the

What I would recommend - and what I use for analysing the ontology with
an external application - is an XML rendering of the ontology, using the
format that the experimental XML format from the File->SaveAs menu.
I've written a tab widget to snap-shot the knowledge base in this XML
format and send it to my analysis application.

The great thing about the XML format is that although all the entries in
it are pretty much Classes and Instances (in fact, I just capture the
Instances) it's very much easier to interpret - and this could be used
to feed a database that is more directly representative of your
application / ontology if XML processing is not an option for your
user's application.



Sent from my BlackBerry(r) wireless device

-----Original Message-----
From: "O'neill, Dennis" <doneill at>

Date: Wed, 18 Feb 2009 17:02:41 
To: User support for Core Protege and the Protege-Frames
editor<protege-discussion at>
Subject: [protege-discussion] Protege 3.3.1 DB Schema

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