[protege-owl] Ontology from database schema?

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[protege-owl] Ontology from database schema?

gremlin
Hi everyone,
 
I'm wondering if there are any tools/prototypes which extract an ontology from a database/database schema.
 
Any pointers in this regard would be appreciated.
 
Regards,
Saqib
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[protege-owl] Re: Ontology from database schema?

Holger Knublauch
Saqib Mir wrote:
 > Hi everyone,
 >
 > I'm wondering if there are any tools/prototypes which extract an
 > ontology from a database/database schema.
 >
 > Any pointers in this regard would be appreciated.

Well, if no one else wants to respond... :)

TopBraid Composer [1] with D2RQ [2] can import arbitrary relational
databases into an OWL or RDF Schema ontology.  The database will be
converted on the fly so that you can treat it like a triple store,
perform reasoning, run SPARQL queries etc.  You can also just save the
generated schema and instances into OWL files, and you can customize the
mapping without writing a single line of code.

For details, see [3] - just give it a try.

Cheers,
Holger

[1] http://www.topbraidcomposer.com/
[2] http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/
[3]
http://composing-the-semantic-web.blogspot.com/2006/08/update-automated-database-import-into.html
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[protege-owl] Re: Ontology from database schema?

Jennifer Vendetti-2
In reply to this post by gremlin
Hello Saqib,

If you installed the "full" version of Protege, you will have a tab
plug-in called "DataGenie" that allows Protege to read data from
arbitrary databases.  You can use JDBC to connect to your database and
move all or portions of your database into Protege.  Tables in your
database will become classes in your ontology and table rows become
instances.

This plug-in was written for Protege-Frames.  If you are interested only
in OWL, you could import your databse into Protege-Frames and then
convert your project to use Protege-OWL.  The source code for this
plug-in is available in our Protege Subversion repository:

http://smi-protege.stanford.edu/svn/datagenie/trunk/

Jennifer

Saqib Mir wrote:

> Hi everyone,
>  
> I'm wondering if there are any tools/prototypes which extract an
> ontology from a database/database schema.
>  
> Any pointers in this regard would be appreciated.
>  
> Regards,
> Saqib


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[protege-owl] Re: Ontology from database schema?

Andreas Langegger
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Hash: SHA1

Hello Jennifer,

is it possible, that the DataGenie plugin does only support the
JDBC-ODBC bridge? I tried to connect to a MySQL database putting the
renamed driver.jar in the protégé root like for database projects.

What's actually the difference between an OWL Database project (when
creating new projects) and the DataGenie tab?

Thanks,
Andy

Jennifer Vendetti wrote:

> Hello Saqib,
>
> If you installed the "full" version of Protege, you will have a tab
> plug-in called "DataGenie" that allows Protege to read data from
> arbitrary databases.  You can use JDBC to connect to your database and
> move all or portions of your database into Protege.  Tables in your
> database will become classes in your ontology and table rows become
> instances.
>
> This plug-in was written for Protege-Frames.  If you are interested only
> in OWL, you could import your databse into Protege-Frames and then
> convert your project to use Protege-OWL.  The source code for this
> plug-in is available in our Protege Subversion repository:
>
> http://smi-protege.stanford.edu/svn/datagenie/trunk/
>
> Jennifer
>
> Saqib Mir wrote:
>
>> Hi everyone,
>>  
>> I'm wondering if there are any tools/prototypes which extract an
>> ontology from a database/database schema.
>>  
>> Any pointers in this regard would be appreciated.
>>  
>> Regards,
>> Saqib
>
>
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>

- --
- ----------------------------------------------------------------------
Dipl.-Ing.(FH) Andreas Langegger
Institute of Applied Knowledge Processing
Johannes Kepler University Linz
A-4040 Linz, Altenberger Straße 69
> http://www.faw.at
> http://www.langegger.at
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[protege-owl] Re: Ontology from database schema?

Andreas Langegger
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Hello,

well. After some trail and error, I would like to post my results and
assumptions for others. Please correct me, if you know that I'm wrong:

* An "OWL/RDF Database" project as described here:
http://protege.stanford.edu/doc/users_guide/projects/saving_a_database_project.html
  _without_ existing sources, allows you to store the unterlaying
Protégé frames model (hence, your Frames or OWL ontology) inside an
JDBC-capable RDBMS. All tables will look like this:
+-------------+--------------+------+-----+---------+-------+
| Field       | Type         | Null | Key | Default | Extra |
+-------------+--------------+------+-----+---------+-------+
| frame       | int(11)      | NO   | MUL | NULL    |       |
| frame_type  | smallint(6)  | NO   |     | NULL    |       |
| slot        | int(11)      | NO   | MUL | NULL    |       |
| facet       | int(11)      | NO   |     | NULL    |       |
| is_template | bit(1)       | NO   |     | NULL    |       |
| value_index | int(11)      | NO   |     | NULL    |       |
| value_type  | smallint(6)  | NO   |     | NULL    |       |
| short_value | varchar(255) | YES  | MUL | NULL    |       |
| long_value  | mediumtext   | YES  |     | NULL    |       |
+-------------+--------------+------+-----+---------+-------+

* ... "with existing sources" assumes this Protégé-prorietary database
scheme which may have been previously created. The feature is not able
to import data from RDBMS using arbirary schemes.

* The DataGenie tab seems to connect to JDBC-ODBC datasources only.
Couldn't test it on Linux.

* To import arbitrary data from RDBMS you could use D2RQ
http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/ which has been
integrated into TopBraidComposer. For Protégé there is no plugin
available yet as far as I know.

regards,
Andy


Andreas Langegger wrote:

> Hello Jennifer,
>
> is it possible, that the DataGenie plugin does only support the
> JDBC-ODBC bridge? I tried to connect to a MySQL database putting the
> renamed driver.jar in the protégé root like for database projects.
>
> What's actually the difference between an OWL Database project (when
> creating new projects) and the DataGenie tab?
>
> Thanks,
> Andy
>
> Jennifer Vendetti wrote:
>>> Hello Saqib,
>>>
>>> If you installed the "full" version of Protege, you will have a tab
>>> plug-in called "DataGenie" that allows Protege to read data from
>>> arbitrary databases.  You can use JDBC to connect to your database and
>>> move all or portions of your database into Protege.  Tables in your
>>> database will become classes in your ontology and table rows become
>>> instances.
>>>
>>> This plug-in was written for Protege-Frames.  If you are interested only
>>> in OWL, you could import your databse into Protege-Frames and then
>>> convert your project to use Protege-OWL.  The source code for this
>>> plug-in is available in our Protege Subversion repository:
>>>
>>> http://smi-protege.stanford.edu/svn/datagenie/trunk/
>>>
>>> Jennifer
>>>
>>> Saqib Mir wrote:
>>>
>>>> Hi everyone,
>>>>  
>>>> I'm wondering if there are any tools/prototypes which extract an
>>>> ontology from a database/database schema.
>>>>  
>>>> Any pointers in this regard would be appreciated.
>>>>  
>>>> Regards,
>>>> Saqib
>>>
>>> -------------------------------------------------------------------------
>>> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>>>
>
> --
> ----------------------------------------------------------------------
> Dipl.-Ing.(FH) Andreas Langegger
> Institute of Applied Knowledge Processing
> Johannes Kepler University Linz
> A-4040 Linz, Altenberger Straße 69
>>> http://www.faw.at
>>> http://www.langegger.at
- -------------------------------------------------------------------------
To unsubscribe go to http://protege.stanford.edu/community/subscribe.html

- --
- ----------------------------------------------------------------------
Dipl.-Ing.(FH) Andreas Langegger
Institute of Applied Knowledge Processing
Johannes Kepler University Linz
A-4040 Linz, Altenberger Straße 69
http://www.faw.at
http://www.langegger.at
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[protege-owl] Re: Ontology from database schema?

Jennifer Vendetti
Administrator
In reply to this post by Andreas Langegger
Hello Andy,

Andreas Langegger wrote:

>Hello Jennifer,
>
>is it possible, that the DataGenie plugin does only support the JDBC-ODBC bridge? I tried to connect to a MySQL database putting the renamed driver.jar in the protégé root like for database projects.
>  
>
Sorry for the delay - I had to look into this a little bit.  The version
of the DataGenie plug-in (version 1.1) that is bundled with Protege only
supports JDBC-ODBC bridge.  However, the University of Washington
(original developers of the plug-in) released a newer version (version
2.0.1) that supports JDBC.  I tried downloading it and it didn't work
out of the box.  So, I fixed a couple of minor bugs to get it working
and posted the new version on our Wiki:

http://protege.cim3.net/cgi-bin/wiki.pl?DataGenie

I was able to successfully connect to a MySQL database and do an import.

Another thing to note - this plug-in was developed before Protege-OWL
existed.  A safer route might be to import your database via the
Protege-Frames editor and then convert to OWL (if you are interested in
OWL).

>What's actually the difference between an OWL Database project (when creating new projects) and the DataGenie tab?
>  
>
The database project type in Protege means that your ontology will be
saved in Protege's databse format.  The DataGenie Tab is a plug-in that
allows you to import data from an arbitrary database into Protege (i.e.,
a database that is not in the Protege format).

Jennifer

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Re: [protege-owl] Ontology from database schema?

Andreas Langegger
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Hi Jennifer,

thanks. I installed the 2.0b version and it worked. As you said, I had
to convert the original Frames project to OWL afterwards.

Also thanks for the information provided on the Wiki.

Regards,
Andy


Jennifer Vendetti wrote:

> Hello Andy,
>
> Andreas Langegger wrote:
>
>> Hello Jennifer,
>>
>> is it possible, that the DataGenie plugin does only support the JDBC-ODBC bridge? I tried to connect to a MySQL database putting the renamed driver.jar in the protégé root like for database projects.
>>  
>>
> Sorry for the delay - I had to look into this a little bit.  The version
> of the DataGenie plug-in (version 1.1) that is bundled with Protege only
> supports JDBC-ODBC bridge.  However, the University of Washington
> (original developers of the plug-in) released a newer version (version
> 2.0.1) that supports JDBC.  I tried downloading it and it didn't work
> out of the box.  So, I fixed a couple of minor bugs to get it working
> and posted the new version on our Wiki:
>
> http://protege.cim3.net/cgi-bin/wiki.pl?DataGenie
>
> I was able to successfully connect to a MySQL database and do an import.
>
> Another thing to note - this plug-in was developed before Protege-OWL
> existed.  A safer route might be to import your database via the
> Protege-Frames editor and then convert to OWL (if you are interested in
> OWL).
>
>> What's actually the difference between an OWL Database project (when creating new projects) and the DataGenie tab?
>>  
>>
> The database project type in Protege means that your ontology will be
> saved in Protege's databse format.  The DataGenie Tab is a plug-in that
> allows you to import data from an arbitrary database into Protege (i.e.,
> a database that is not in the Protege format).
>
> Jennifer
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl

- --
- ----------------------------------------------------------------------
Dipl.-Ing.(FH) Andreas Langegger
Institute of Applied Knowledge Processing
Johannes Kepler University Linz
A-4040 Linz, Altenberger Straße 69
> http://www.faw.at
> http://www.langegger.at
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