Protege 3.3.1 DB Schema

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Protege 3.3.1 DB Schema

O'Neill, Dennis

What is the schema definition for the database version of a Protégé ontology? I have a user who wants to parse/filter the contents for a specific application and the Access Protégé.mdb file is a bit difficult to puzzle out. In particular what are the frame_type, slot, value_index and value_type attributes and how do they relate?

 

Dennis M. O'Neill
SAIC
Contractor to Marathon Oil Company
Enterprise Content Management
Room 2068D
(281) 236-5690 (Cell)
[hidden email]

 


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Re: Protege 3.3.1 DB Schema

Jonathan Carter-8
Hi Dennis,

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

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 indexes)

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.

Regards

Jonathan


Sent from my BlackBerry® wireless device

-----Original Message-----
From: "O'neill, Dennis" <[hidden email]>

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


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Re: Protege 3.3.1 DB Schema

O'Neill, Dennis
Jonathan,

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?

Thanks,

Dennis

Dennis M. O'Neill
SAIC
Contractor to Marathon Oil Company
Enterprise Content Management
Room 2068D
(281) 236-5690 (Cell)
[hidden email]
-----Original Message-----
From: [hidden email]
[mailto:[hidden email]] 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:
singular).

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
indexes)

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.

Regards

Jonathan


Sent from my BlackBerry(r) wireless device

-----Original Message-----
From: "O'neill, Dennis" <[hidden email]>

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


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Re: Protege 3.3.1 DB Schema

Jonathan Carter-8

Hi Dennis,

Makes sense. I don't have any documentation for the structure that is used, although there are only about 7 or 8 columns in the table and you are right you can decipher what each does from the source code. (I had an extensive look around in there trying to resolve the SQLServer 2005 issue.

Have a look at the code in the protege/storage/database classes:

http://smi-protege.stanford.edu/svn/protege-core/trunk/src/edu/stanford/smi/protege/storage/database/

In particular, the class of interest used to be DatabaseFrameDB.java but things have been refactored. To see what's in Protege 3.3.1, go back to a version in the subversion repository that's about January 2008:

http://smi-protege.stanford.edu/svn/protege-core/branches/namespace/src/edu/stanford/smi/protege/storage/database/DatabaseFrameDb.java?rev=8708&view=markup

Hope this helps


Regards

Jonathan

Quoting "O'neill, Dennis" <[hidden email]>:

> Jonathan,
>
> 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?
>
> Thanks,
>
> Dennis
>
> Dennis M. O'Neill
> SAIC
> Contractor to Marathon Oil Company
> Enterprise Content Management
> Room 2068D
> (281) 236-5690 (Cell)
> [hidden email]
> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] 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:
> singular).
>
> 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
> indexes)
>
> 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.
>
> Regards
>
> Jonathan
>
>
> Sent from my BlackBerry(r) wireless device
>
> -----Original Message-----
> From: "O'neill, Dennis" <[hidden email]>
>
> Date: Wed, 18 Feb 2009 17:02:41
> To: User support for Core Protege and the Protege-Frames
> editor<[hidden email]>
> Subject: [protege-discussion] Protege 3.3.1 DB Schema
>
>
> _______________________________________________
> protege-discussion mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>
> _______________________________________________
> protege-discussion mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>

_______________________________________

Jonathan Carter - Head of Technical Architecture
Enterprise Architecture Solutions Ltd

Web: www.enterprise-architecture.com
_______________________________________

Assess your EA maturity at:
www.enterprise-architecture.com/EAvaluator
_______________________________________

W O R L D    C L A S S    A R C H I T E C T U R E


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Re: Protege 3.3.1 DB Schema

Jennifer Vendetti
Administrator
In reply to this post by O'Neill, Dennis
Hello Dennis,

O'neill, Dennis wrote:

What is the schema definition for the database version of a Protégé ontology?


We have some documentation on the website that describes the rationale for the database design.  It includes descriptions of the various columns:

http://protege.stanford.edu/doc/design/jdbc_backend.html

I have a user who wants to parse/filter the contents for a specific application and the Access Protégé.mdb file is a bit difficult to puzzle out. In particular what are the frame_type, slot, value_index and value_type attributes and how do they relate?


We generally recommend against this approach in favor of just using the Protege API to access whatever part of the ontology you need to work with.  The API is also documented on our website:

http://protege.stanford.edu/doc/dev.html

Jennifer


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Re: Protege 3.3.1 DB Schema

Jennifer Vendetti
Administrator
In reply to this post by O'Neill, Dennis
Hello Dennis,

O'neill, Dennis wrote:
> 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.
>  

You might consider modularizing your ontology.  There is a plug-in
called "PROMPT" that can (among other things) assist you in extracting
portions of your ontology:

http://protegewiki.stanford.edu/index.php/PROMPT

In Protege 3.3.1, the project inclusion mechanism was not supported for
ontologies stored in Protege's database back-end, but this is now
supported in Protege 3.4.

> 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.
>  

Perhaps writing an export plug-in for this task would work:

http://protege.stanford.edu/doc/pdk/plugins/export_plugin.html

Jennifer

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Re: Protege 3.3.1 DB Schema

O'Neill, Dennis

Jennifer,

 

I have been able to successfully create a Protégé DB version with MS Access running on my local machine; but when I try to write to a SQL Server DB running on another machine, things seem to get lost in the woods. It may have to do with the driver I am specifying, but not being a ODBC expert (or even novice) I could use a bit of help. Here is what the ODBC Admin Tool has to say about the setup

 

 

 

I then try to configure in Protégé as follows:

 

 

It appears to connect to the DB OK (subsequent runs say the Table ProtegeOrg already exists), it reports a certain number of frames are to be written (about 4600 in this case), it begins sending INFO messages for every 1000 it writes out, but then it bombs out with a stack trace as follows:

 

INFO: Getting 4368 frames, please be patient, Fri Feb 27 10:25:40 CST 2009

INFO: 1000/4368, Fri Feb 27 10:25:55 CST 2009, delta=14, mem(f/t/m)=66818/99352/497418

INFO: 2000/4368, Fri Feb 27 10:26:12 CST 2009, delta=16, mem(f/t/m)=66878/99352/497418

INFO: 3000/4368, Fri Feb 27 10:26:32 CST 2009, delta=20, mem(f/t/m)=66922/99352/497418

INFO: 4000/4368, Fri Feb 27 10:26:51 CST 2009, delta=18, mem(f/t/m)=71571/99352/497418

INFO: java.sql.SQLException: [Microsoft][ODBC SQL Server Driver]Invalid Descriptor Index

        at sun.jdbc.odbc.JdbcOdbc.createSQLException(JdbcOdbc.java:6958)

        at sun.jdbc.odbc.JdbcOdbc.standardError(JdbcOdbc.java:7115)

        at sun.jdbc.odbc.JdbcOdbc.SQLGetDataString(JdbcOdbc.java:3908)

        at sun.jdbc.odbc.JdbcOdbcResultSet.getDataString(JdbcOdbcResultSet.java:5699)

        at sun.jdbc.odbc.JdbcOdbcResultSet.getString(JdbcOdbcResultSet.java:353)

        at edu.stanford.smi.protege.storage.database.DatabaseUtils.getShortValue(Unknown Source)

        at edu.stanford.smi.protege.storage.database.DatabaseFrameDb.getShortValue(Unknown Source)

        at edu.stanford.smi.protege.storage.database.DatabaseFrameDb.getFrameValuesSQL(Unknown Source)

        at edu.stanford.smi.protege.storage.database.DatabaseFrameDb.getFrameValues(Unknown Source)

        at edu.stanford.smi.protege.storage.database.ValueCachingNarrowFrameStore.loadFrameIntoCache(Unknown Source)

        at edu.stanford.smi.protege.storage.database.ValueCachingNarrowFrameStore.getValues(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.MergingNarrowFrameStore.getValues(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.MergingNarrowFrameStore.getValues(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.ClosureCachingBasicFrameStore.getValues(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.SimpleFrameStore.getValue(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.SimpleFrameStore.getDirectOwnSlotValue(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.SimpleFrameStore.getFrameName(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.ModificationFrameStore.getFrameName(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.ModificationFrameStore.getFrameName(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.getFrameName(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.ModificationFrameStore.getFrameName(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getFrameName(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getFrameName(Unknown Source)

        at edu.stanford.smi.protege.model.DefaultKnowledgeBase.getName(Unknown Source)

        at edu.stanford.smi.protege.model.DefaultFrame.getName(Unknown Source)

        at edu.stanford.smi.protege.model.DefaultCls.toString(Unknown Source)

        at java.lang.String.valueOf(String.java:2615)

        at java.util.AbstractCollection.toString(AbstractCollection.java:454)

        at java.lang.String.valueOf(String.java:2615)

        at java.lang.StringBuilder.append(StringBuilder.java:116)

        at edu.stanford.smi.protege.util.LazyTreeNode.toString(Unknown Source)

        at javax.swing.JTree.convertValueToText(JTree.java:1139)

        at javax.swing.tree.DefaultTreeCellRenderer.getTreeCellRendererComponent(DefaultTreeCellRenderer.java:331)

        at javax.swing.plaf.basic.BasicTreeUI$NodeDimensionsHandler.getNodeDimensions(BasicTreeUI.java:2693)

        at javax.swing.tree.AbstractLayoutCache.getNodeDimensions(AbstractLayoutCache.java:475)

        at javax.swing.tree.VariableHeightLayoutCache$TreeStateNode.updatePreferredSize(VariableHeightLayoutCache.java:1342)

        at javax.swing.tree.VariableHeightLayoutCache.rebuild(VariableHeightLayoutCache.java:720)

        at javax.swing.tree.VariableHeightLayoutCache.setModel(VariableHeightLayoutCache.java:91)

        at javax.swing.plaf.basic.BasicTreeUI.setModel(BasicTreeUI.java:400)

        at javax.swing.plaf.basic.BasicTreeUI$Handler.propertyChange(BasicTreeUI.java:3388)

        at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:333)

        at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:270)

        at java.awt.Component.firePropertyChange(Component.java:7192)

        at javax.swing.JTree.setModel(JTree.java:710)

        at javax.swing.JTree.<init>(JTree.java:511)

        at edu.stanford.smi.protege.util.SelectableTree.<init>(Unknown Source)

        at edu.stanford.smi.protege.util.ComponentFactory.createSelectableTree(Unknown Source)

        at edu.stanford.smi.protege.ui.SubclassPane.createSelectableTree(Unknown Source)

        at edu.stanford.smi.protege.ui.SubclassPane.<init>(Unknown Source)

        at edu.stanford.smi.protege.ui.ClsesPanel.createSubclassPane(Unknown Source)

        at edu.stanford.smi.protege.ui.ClsesPanel.createPanes(Unknown Source)

        at edu.stanford.smi.protege.ui.ClsesPanel.<init>(Unknown Source)

        at edu.stanford.smi.protege.widget.ClsesTab.createClsesPanel(Unknown Source)

        at edu.stanford.smi.protege.widget.ClsesTab.createClsesSplitter(Unknown Source)

        at edu.stanford.smi.protege.widget.ClsesTab.createMainSplitter(Unknown Source)

        at edu.stanford.smi.protege.widget.ClsesTab.initialize(Unknown Source)

        at edu.stanford.smi.protege.widget.WidgetUtilities.createTabWidget(Unknown Source)

        at edu.stanford.smi.protege.ui.ProjectView.addTab(Unknown Source)

        at edu.stanford.smi.protege.ui.ProjectView.createTabbedPane(Unknown Source)

        at edu.stanford.smi.protege.ui.ProjectView.<init>(Unknown Source)

        at edu.stanford.smi.protege.ui.ProjectManager.displayCurrentProject(Unknown Source)

        at edu.stanford.smi.protege.ui.ProjectManager.displayCurrentProject(Unknown Source)

        at edu.stanford.smi.protege.ui.ProjectManager.loadProject(Unknown Source)

        at edu.stanford.smi.protege.ui.ProjectManager.changeProjectStorageFormatRequest(Unknown Source)

        at edu.stanford.smi.protege.action.ChangeProjectStorageFormat.actionPerformed(Unknown Source)

        at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)

        at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2169)

        at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)

        at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)

        at javax.swing.AbstractButton.doClick(AbstractButton.java:302)

        at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1051)

        at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1092)

        at java.awt.Component.processMouseEvent(Component.java:5517)

        at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)

        at java.awt.Component.processEvent(Component.java:5282)

        at java.awt.Container.processEvent(Container.java:1966)

        at java.awt.Component.dispatchEventImpl(Component.java:3984)

        at java.awt.Container.dispatchEventImpl(Container.java:2024)

        at java.awt.Component.dispatchEvent(Component.java:3819)

        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)

        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892)

        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)

        at java.awt.Container.dispatchEventImpl(Container.java:2010)

        at java.awt.Window.dispatchEventImpl(Window.java:1791)

        at java.awt.Component.dispatchEvent(Component.java:3819)

        at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)

        at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)

        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)

        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)

        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)

        at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

 

WARNING: java.lang.RuntimeException: [Microsoft][ODBC SQL Server Driver]Invalid Descriptor Index

        at edu.stanford.smi.protege.storage.database.DatabaseFrameDb.createRuntimeException(Unknown Source)

        at edu.stanford.smi.protege.storage.database.DatabaseFrameDb.getFrameValues(Unknown Source)

        at edu.stanford.smi.protege.storage.database.ValueCachingNarrowFrameStore.loadFrameIntoCache(Unknown Source)

        at edu.stanford.smi.protege.storage.database.ValueCachingNarrowFrameStore.getValues(Unknown Source)

 

It goes on with the “Invalid descriptor” error a total of 6 or 7 times. It then tries to redisplay the Java window and barfs with a couple of

 

-- WidgetUtilities.createTabWidget()

INFO: java.sql.SQLException: [Microsoft][ODBC SQL Server Driver]Connection is busy with results for another hstmt

        at sun.jdbc.odbc.JdbcOdbc.createSQLException(JdbcOdbc.java:6958)

        at sun.jdbc.odbc.JdbcOdbc.standardError(JdbcOdbc.java:7115)

        at sun.jdbc.odbc.JdbcOdbc.SQLExecute(JdbcOdbc.java:3150)

        at sun.jdbc.odbc.JdbcOdbcPreparedStatement.execute(JdbcOdbcPreparedStatement.java:214)

        at sun.jdbc.odbc.JdbcOdbcPreparedStatement.executeQuery(JdbcOdbcPreparedStatement.java:89)

        at edu.stanford.smi.protege.storage.database.DatabaseFrameDb.executeQuery(Unknown Source)

        at edu.stanford.smi.protege.storage.database.DatabaseFrameDb.getFrameValuesSQL(Unknown Source)

        at edu.stanford.smi.protege.storage.database.DatabaseFrameDb.getFrameValues(Unknown Source)

        at edu.stanford.smi.protege.storage.database.ValueCachingNarrowFrameStore.loadFrameIntoCache(Unknown Source)

        at edu.stanford.smi.protege.storage.database.ValueCachingNarrowFrameStore.getValues(Unknown Source)

        at edu.stanford.smi.protege.model.framestore.MergingNarrowFrameStore.getValues(Unknown Source)

 

And draws a Protégé window that looks like

 

 

When I go to exit, it asks if I want to save. If I say yes, it dies with

 

 

Any suggestions?

 

Dennis M. O'Neill

SAIC

Contractor to Marathon Oil Company

Enterprise Content Management

Room 2068D

(281) 236-5690 (Cell)

[hidden email]

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Jennifer Vendetti
Sent: Monday, February 23, 2009 7:50 PM
To: User support for Core Protege and the Protege-Frames editor
Subject: Re: [protege-discussion] Protege 3.3.1 DB Schema

 

Hello Dennis,

 

O'neill, Dennis wrote:

> 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.

>  

 

You might consider modularizing your ontology.  There is a plug-in

called "PROMPT" that can (among other things) assist you in extracting

portions of your ontology:

 

http://protegewiki.stanford.edu/index.php/PROMPT

 

In Protege 3.3.1, the project inclusion mechanism was not supported for

ontologies stored in Protege's database back-end, but this is now

supported in Protege 3.4.

 

> 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.

>  

 

Perhaps writing an export plug-in for this task would work:

 

http://protege.stanford.edu/doc/pdk/plugins/export_plugin.html

 

Jennifer

 

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Re: Protege 3.3.1 DB Schema

Tania Tudorache
Dennis,

Documentation about the database format used by the Protege backend is here:

http://protege.stanford.edu/doc/design/jdbc_backend.html

This page has been written a long time ago, and now the backend uses for
the frame, slot and facet column the full name of the entity rather than
an integer.

I do not recommend that you do anything at the database level. Rather,
you can implement a export plugin using the Protege API to whatever
format you need. Other option is to export the entire content of the
ontology using the QueryTab to a CSV file and postprocess that.

Another thing is that you should not use the JDBC ODBC bridge. It has
very bad performance. Instead you should copy the database driver in the
protege installation directory and use directly that driver. We have
detailed instructions here:

http://protegewiki.stanford.edu/index.php/PrF_UG_files_database_backend

Tania



O'neill, Dennis wrote:

>
> Jennifer,
>
> I have been able to successfully create a Protégé DB version with MS
> Access running on my local machine; but when I try to write to a SQL
> Server DB running on another machine, things seem to get lost in the
> woods. It may have to do with the driver I am specifying, but not
> being a ODBC expert (or even novice) I could use a bit of help. Here
> is what the ODBC Admin Tool has to say about the setup
>
> I then try to configure in Protégé as follows:
>
> It appears to connect to the DB OK (subsequent runs say the Table
> ProtegeOrg already exists), it reports a certain number of frames are
> to be written (about 4600 in this case), it begins sending INFO
> messages for every 1000 it writes out, but then it bombs out with a
> stack trace as follows:
>
> INFO: Getting 4368 frames, please be patient, Fri Feb 27 10:25:40 CST 2009
>
> INFO: 1000/4368, Fri Feb 27 10:25:55 CST 2009, delta=14,
> mem(f/t/m)=66818/99352/497418
>
> INFO: 2000/4368, Fri Feb 27 10:26:12 CST 2009, delta=16,
> mem(f/t/m)=66878/99352/497418
>
> INFO: 3000/4368, Fri Feb 27 10:26:32 CST 2009, delta=20,
> mem(f/t/m)=66922/99352/497418
>
> INFO: 4000/4368, Fri Feb 27 10:26:51 CST 2009, delta=18,
> mem(f/t/m)=71571/99352/497418
>
> INFO: java.sql.SQLException: [Microsoft][ODBC SQL Server
> Driver]Invalid Descriptor Index
>
> at sun.jdbc.odbc.JdbcOdbc.createSQLException(JdbcOdbc.java:6958)
>
> at sun.jdbc.odbc.JdbcOdbc.standardError(JdbcOdbc.java:7115)
>
> at sun.jdbc.odbc.JdbcOdbc.SQLGetDataString(JdbcOdbc.java:3908)
>
> at
> sun.jdbc.odbc.JdbcOdbcResultSet.getDataString(JdbcOdbcResultSet.java:5699)
>
> at sun.jdbc.odbc.JdbcOdbcResultSet.getString(JdbcOdbcResultSet.java:353)
>
> at
> edu.stanford.smi.protege.storage.database.DatabaseUtils.getShortValue(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.storage.database.DatabaseFrameDb.getShortValue(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.storage.database.DatabaseFrameDb.getFrameValuesSQL(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.storage.database.DatabaseFrameDb.getFrameValues(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.storage.database.ValueCachingNarrowFrameStore.loadFrameIntoCache(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.storage.database.ValueCachingNarrowFrameStore.getValues(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.model.framestore.MergingNarrowFrameStore.getValues(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.model.framestore.MergingNarrowFrameStore.getValues(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.model.framestore.ClosureCachingBasicFrameStore.getValues(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.model.framestore.SimpleFrameStore.getValue(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.model.framestore.SimpleFrameStore.getDirectOwnSlotValue(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.model.framestore.SimpleFrameStore.getFrameName(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.model.framestore.ModificationFrameStore.getFrameName(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.model.framestore.ModificationFrameStore.getFrameName(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.getFrameName(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.model.framestore.ModificationFrameStore.getFrameName(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getFrameName(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getFrameName(Unknown
> Source)
>
> at edu.stanford.smi.protege.model.DefaultKnowledgeBase.getName(Unknown
> Source)
>
> at edu.stanford.smi.protege.model.DefaultFrame.getName(Unknown Source)
>
> at edu.stanford.smi.protege.model.DefaultCls.toString(Unknown Source)
>
> at java.lang.String.valueOf(String.java:2615)
>
> at java.util.AbstractCollection.toString(AbstractCollection.java:454)
>
> at java.lang.String.valueOf(String.java:2615)
>
> at java.lang.StringBuilder.append(StringBuilder.java:116)
>
> at edu.stanford.smi.protege.util.LazyTreeNode.toString(Unknown Source)
>
> at javax.swing.JTree.convertValueToText(JTree.java:1139)
>
> at
> javax.swing.tree.DefaultTreeCellRenderer.getTreeCellRendererComponent(DefaultTreeCellRenderer.java:331)
>
> at
> javax.swing.plaf.basic.BasicTreeUI$NodeDimensionsHandler.getNodeDimensions(BasicTreeUI.java:2693)
>
> at
> javax.swing.tree.AbstractLayoutCache.getNodeDimensions(AbstractLayoutCache.java:475)
>
> at
> javax.swing.tree.VariableHeightLayoutCache$TreeStateNode.updatePreferredSize(VariableHeightLayoutCache.java:1342)
>
> at
> javax.swing.tree.VariableHeightLayoutCache.rebuild(VariableHeightLayoutCache.java:720)
>
> at
> javax.swing.tree.VariableHeightLayoutCache.setModel(VariableHeightLayoutCache.java:91)
>
> at javax.swing.plaf.basic.BasicTreeUI.setModel(BasicTreeUI.java:400)
>
> at
> javax.swing.plaf.basic.BasicTreeUI$Handler.propertyChange(BasicTreeUI.java:3388)
>
> at
> java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:333)
>
> at
> java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:270)
>
> at java.awt.Component.firePropertyChange(Component.java:7192)
>
> at javax.swing.JTree.setModel(JTree.java:710)
>
> at javax.swing.JTree.<init>(JTree.java:511)
>
> at edu.stanford.smi.protege.util.SelectableTree.<init>(Unknown Source)
>
> at
> edu.stanford.smi.protege.util.ComponentFactory.createSelectableTree(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.ui.SubclassPane.createSelectableTree(Unknown
> Source)
>
> at edu.stanford.smi.protege.ui.SubclassPane.<init>(Unknown Source)
>
> at edu.stanford.smi.protege.ui.ClsesPanel.createSubclassPane(Unknown
> Source)
>
> at edu.stanford.smi.protege.ui.ClsesPanel.createPanes(Unknown Source)
>
> at edu.stanford.smi.protege.ui.ClsesPanel.<init>(Unknown Source)
>
> at edu.stanford.smi.protege.widget.ClsesTab.createClsesPanel(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.widget.ClsesTab.createClsesSplitter(Unknown
> Source)
>
> at edu.stanford.smi.protege.widget.ClsesTab.createMainSplitter(Unknown
> Source)
>
> at edu.stanford.smi.protege.widget.ClsesTab.initialize(Unknown Source)
>
> at
> edu.stanford.smi.protege.widget.WidgetUtilities.createTabWidget(Unknown
> Source)
>
> at edu.stanford.smi.protege.ui.ProjectView.addTab(Unknown Source)
>
> at edu.stanford.smi.protege.ui.ProjectView.createTabbedPane(Unknown
> Source)
>
> at edu.stanford.smi.protege.ui.ProjectView.<init>(Unknown Source)
>
> at
> edu.stanford.smi.protege.ui.ProjectManager.displayCurrentProject(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.ui.ProjectManager.displayCurrentProject(Unknown
> Source)
>
> at edu.stanford.smi.protege.ui.ProjectManager.loadProject(Unknown Source)
>
> at
> edu.stanford.smi.protege.ui.ProjectManager.changeProjectStorageFormatRequest(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.action.ChangeProjectStorageFormat.actionPerformed(Unknown
> Source)
>
> at
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)
>
> at
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2169)
>
> at
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
>
> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
>
> at javax.swing.AbstractButton.doClick(AbstractButton.java:302)
>
> at
> javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1051)
>
> at
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1092)
>
> at java.awt.Component.processMouseEvent(Component.java:5517)
>
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)
>
> at java.awt.Component.processEvent(Component.java:5282)
>
> at java.awt.Container.processEvent(Container.java:1966)
>
> at java.awt.Component.dispatchEventImpl(Component.java:3984)
>
> at java.awt.Container.dispatchEventImpl(Container.java:2024)
>
> at java.awt.Component.dispatchEvent(Component.java:3819)
>
> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)
>
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892)
>
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)
>
> at java.awt.Container.dispatchEventImpl(Container.java:2010)
>
> at java.awt.Window.dispatchEventImpl(Window.java:1791)
>
> at java.awt.Component.dispatchEvent(Component.java:3819)
>
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>
> at
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)
>
> at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
>
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
>
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
>
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>
> WARNING: java.lang.RuntimeException: [Microsoft][ODBC SQL Server
> Driver]Invalid Descriptor Index
>
> at
> edu.stanford.smi.protege.storage.database.DatabaseFrameDb.createRuntimeException(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.storage.database.DatabaseFrameDb.getFrameValues(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.storage.database.ValueCachingNarrowFrameStore.loadFrameIntoCache(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.storage.database.ValueCachingNarrowFrameStore.getValues(Unknown
> Source)
>
> It goes on with the “Invalid descriptor” error a total of 6 or 7
> times. It then tries to redisplay the Java window and barfs with a
> couple of
>
> -- WidgetUtilities.createTabWidget()
>
> INFO: java.sql.SQLException: [Microsoft][ODBC SQL Server
> Driver]Connection is busy with results for another hstmt
>
> at sun.jdbc.odbc.JdbcOdbc.createSQLException(JdbcOdbc.java:6958)
>
> at sun.jdbc.odbc.JdbcOdbc.standardError(JdbcOdbc.java:7115)
>
> at sun.jdbc.odbc.JdbcOdbc.SQLExecute(JdbcOdbc.java:3150)
>
> at
> sun.jdbc.odbc.JdbcOdbcPreparedStatement.execute(JdbcOdbcPreparedStatement.java:214)
>
> at
> sun.jdbc.odbc.JdbcOdbcPreparedStatement.executeQuery(JdbcOdbcPreparedStatement.java:89)
>
> at
> edu.stanford.smi.protege.storage.database.DatabaseFrameDb.executeQuery(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.storage.database.DatabaseFrameDb.getFrameValuesSQL(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.storage.database.DatabaseFrameDb.getFrameValues(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.storage.database.ValueCachingNarrowFrameStore.loadFrameIntoCache(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.storage.database.ValueCachingNarrowFrameStore.getValues(Unknown
> Source)
>
> at
> edu.stanford.smi.protege.model.framestore.MergingNarrowFrameStore.getValues(Unknown
> Source)
>
> And draws a Protégé window that looks like
>
> When I go to exit, it asks if I want to save. If I say yes, it dies with
>
> Any suggestions?
>
> Dennis M. O'Neill
>
> SAIC
>
> Contractor to Marathon Oil Company
>
> Enterprise Content Management
>
> Room 2068D
>
> (281) 236-5690 (Cell)
>
> [hidden email]
>
> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of
> Jennifer Vendetti
> Sent: Monday, February 23, 2009 7:50 PM
> To: User support for Core Protege and the Protege-Frames editor
> Subject: Re: [protege-discussion] Protege 3.3.1 DB Schema
>
> Hello Dennis,
>
> O'neill, Dennis wrote:
>
> > 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.
>
> >
>
> You might consider modularizing your ontology. There is a plug-in
>
> called "PROMPT" that can (among other things) assist you in extracting
>
> portions of your ontology:
>
> http://protegewiki.stanford.edu/index.php/PROMPT
>
> In Protege 3.3.1, the project inclusion mechanism was not supported for
>
> ontologies stored in Protege's database back-end, but this is now
>
> supported in Protege 3.4.
>
> > 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.
>
> >
>
> Perhaps writing an export plug-in for this task would work:
>
> http://protege.stanford.edu/doc/pdk/plugins/export_plugin.html
>
> Jennifer
>
> _______________________________________________
>
> protege-discussion mailing list
>
> [hidden email]
>
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> protege-discussion mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>  

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(no subject)

Vbertaud
Hi,

I tried to open the Foundational Model of Anatomy (FMA)  in OWL (fma20OWLDLcomponent.owl) after download from
http://www.bioontology.org/wiki/index.php/FMAInOwl.

After loading 90 000 triples, the protege window displays an error message:

Exception occured during event dispatching:
java.lang.OutOfMemoryError: PermGen space

How come and how can I fix it?

I 've already tried to change the heap size max in the protege.lax file to 800 000 000. But it still doesn't work. The error message appear after loading 134 000 triples. Shall I enhance the heap size max again?

(I am using Protege3.4.)

Thanks in advance

Valérie BERTAUD

-------------------------------------------------------------------------------------------
Dr Valérie BERTAUD
Chirurgien-Dentiste, Maitre de Conférence-Praticien Hospitalier

Ingénieur en Informatique
Docteur de l'Université de Rennes 1 Mention Biologie et Sciences de la Santé

UFR d'Odontologie de Rennes - 2, Avenue du Professeur Léon Bernard (Bat 15) - F-35043 Rennes Cedex

CHRU de Rennes - 2 Place Pasteur, 35033 Rennes Cedex 9

Laboratoire d’Informatique Médicale - Equipe d’Accueil 3888 : Modélisation conceptuelle des connaissances biomédicales, Faculté de Médecin e de Rennes, Université de Rennes1, 2 rue Henri Le Guilloux - 35000 Rennes.
e-mail: [hidden email]
Tel: 06-76-66-28-62




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Re: (no subject)

Csongor Nyulas
Administrator
Yes, you should increase the memory even more. That's the only thing you
can do if you want to open the ontology from file.

Csongor

[hidden email] wrote:

> Hi,
>
> I tried to open the Foundational Model of Anatomy (FMA)  in OWL
> (fma20OWLDLcomponent.owl) after download from
> http://www.bioontology.org/wiki/index.php/FMAInOwl.
>
> After loading 90 000 triples, the protege window displays an error
> message:
>
> Exception occured during event dispatching:
> java.lang.OutOfMemoryError: PermGen space
>
> How come and how can I fix it?
>
> I 've already tried to change the heap size max in the protege.lax
> file to 800 000 000. But it still doesn't work. The error message
> appear after loading 134 000 triples. Shall I enhance the heap size
> max again?
>
> (I am using Protege3.4.)
>
> Thanks in advance
>
> Valérie BERTAUD
>
> -------------------------------------------------------------------------------------------
> Dr Valérie BERTAUD
> Chirurgien-Dentiste, Maitre de Conférence-Praticien Hospitalier
>
> Ingénieur en Informatique
> Docteur de l'Université de Rennes 1 Mention Biologie et Sciences de la
> Santé
>
> UFR d'Odontologie de Rennes - 2, Avenue du Professeur Léon Bernard
> (Bat 15) - F-35043 Rennes Cedex
>
> CHRU de Rennes - 2 Place Pasteur, 35033 Rennes Cedex 9
>
> Laboratoire d’Informatique Médicale - Equipe d’Accueil 3888 :
> Modélisation conceptuelle des connaissances biomédicales, Faculté de
> Médecin e de Rennes, Université de Rennes1, 2 rue Henri Le Guilloux -
> 35000 Rennes.
> e-mail: [hidden email]
> Tel: 06-76-66-28-62
>
>
>
>
> ------------------------------------------------------------------------
> *Reçevez AOL Mail sur votre téléphone.*Vos e-mails accessibles à tout
> moment! Créez <http://services.aol.fr/webmail/> un e-mail gratuit
> aujourd’hui.
> ------------------------------------------------------------------------
>
> _______________________________________________
> protege-discussion mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>  

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Re: (no subject)

Safran, Tracy (NIH/NCI) [C]
You need to specifically increase PermGen space.  Java option -XX:MaxPermSize=256M

Tracy M. Safran
Contractor - SAIC Frederick
EVS support
301-402-1537


-----Original Message-----
From: Csongor Nyulas [mailto:[hidden email]]
Sent: Friday, March 06, 2009 5:44 PM
To: User support for Core Protege and the Protege-Frames editor
Subject: Re: [protege-discussion] (no subject)

Yes, you should increase the memory even more. That's the only thing you
can do if you want to open the ontology from file.

Csongor

[hidden email] wrote:

> Hi,
>
> I tried to open the Foundational Model of Anatomy (FMA)  in OWL
> (fma20OWLDLcomponent.owl) after download from
> http://www.bioontology.org/wiki/index.php/FMAInOwl.
>
> After loading 90 000 triples, the protege window displays an error
> message:
>
> Exception occured during event dispatching:
> java.lang.OutOfMemoryError: PermGen space
>
> How come and how can I fix it?
>
> I 've already tried to change the heap size max in the protege.lax
> file to 800 000 000. But it still doesn't work. The error message
> appear after loading 134 000 triples. Shall I enhance the heap size
> max again?
>
> (I am using Protege3.4.)
>
> Thanks in advance
>
> Valérie BERTAUD
>
> -------------------------------------------------------------------------------------------
> Dr Valérie BERTAUD
> Chirurgien-Dentiste, Maitre de Conférence-Praticien Hospitalier
>
> Ingénieur en Informatique
> Docteur de l'Université de Rennes 1 Mention Biologie et Sciences de la
> Santé
>
> UFR d'Odontologie de Rennes - 2, Avenue du Professeur Léon Bernard
> (Bat 15) - F-35043 Rennes Cedex
>
> CHRU de Rennes - 2 Place Pasteur, 35033 Rennes Cedex 9
>
> Laboratoire d’Informatique Médicale - Equipe d’Accueil 3888 :
> Modélisation conceptuelle des connaissances biomédicales, Faculté de
> Médecin e de Rennes, Université de Rennes1, 2 rue Henri Le Guilloux -
> 35000 Rennes.
> e-mail: [hidden email]
> Tel: 06-76-66-28-62
>
>
>
>
> ------------------------------------------------------------------------
> *Reçevez AOL Mail sur votre téléphone.*Vos e-mails accessibles à tout
> moment! Créez <http://services.aol.fr/webmail/> un e-mail gratuit
> aujourd’hui.
> ------------------------------------------------------------------------
>
> _______________________________________________
> protege-discussion mailing list
> [hidden email]
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