owldb-users — This list enables user discussion

[Owldb-users] Using OWLDB for large ontologies

[Chahd C. <cha...@gm...>]

Hi,
Can we use OWLDB to store very big ontologies?
thank you

[Owldb-users] Fwd: Problem using OWLDB inside JBoss

[Jörg H. <He...@ki...>]

Hi,
i hope you have used the classpath for the hibernate.cfg.xml. It should also be deployed on the server!

Your problem might come from the fact, that owldb is not based on JPA and we don't use an EntityManager.

greets


> Von: Chowdary Davuluri <dvr...@gm...>
> Datum: 4. Februar 2010 09:57:25 MEZ
> An: Jörg Henß <He...@ki...>
> Betreff: Re: [Owldb-users] Problem using OWLDB inside JBoss
> 
> Hi,
> Sorry, I couldn't give you the earlier stack trace, as I am facing a different problem now after switching to a new work space. I get the following exception even though I made sure that the directory containing hibernate.cfg.xml is added to my path variable.
> 
> "Caused by: org.hibernate.HibernateException: /hibernate.cfg.xml not found"
> 
> Here's my code:-
> @Stateless
> public class OntologyDBManagerBean implements OntologyDBManagerLocal,OntologyDBManagerRemote{
>     private OWLOntologyManager manager;
>     private OWLOntology ontology;
>     
>     @Override
>     public void setupDBManager() {
>         try{
>         manager=OWLDBManager.createOWLOntologyManager();
>         URL ontology_url=getClass().getResource("/net/massmatrix/metadb/core/MetaDB.owl");
>         URI ontology_uri=new URI(ontology_url.toString().replace(" ","%20"));
> 
>         ontology=manager.loadOntologyFromPhysicalURI(ontology_uri);
>         
>         URI db_uri=URI.create("jdbc:mysql://localhost/owldb");
>         OWLDBOntologyFormat format=new OWLDBOntologyFormat();
>         OWLDBOntologyOutputTarget target_db=new OWLDBOntologyOutputTarget(db_uri);
>         manager.saveOntology(ontology,format,target_db);
>         }catch(URISyntaxException e){
>             System.out.println("Error converting the URL to an URI");
>             e.printStackTrace();
>         }catch(OWLOntologyCreationException e){
>             System.out.println("Error creating the ontology from the URI specified");
>             e.printStackTrace();
>         }catch(OWLOntologyStorageException e){
>             System.out.println("Error while saving the ontology");
>             e.printStackTrace();
>         }
>     }
> }
> 
> 
> Can you help me fix this ?
> 
> Thanks,
> Chowdary Davuluri
> 
> On Wed, Feb 3, 2010 at 8:58 AM, Jörg Henß <He...@ki...> wrote:
> Hello Chowdary,
> 
> could you provide us more details about your Problem? E.g. a stacktrace when an error occurs?
> Perhaps http://docs.jboss.org/jbossas/getting_started/v4/html/hibernate.html can help you withe the integration of the owldb code.
> My best guess is that there are also problem with the use of JNDI and the context lookup.
> 
> greets
> Joerg
> 
> 
> 
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> 
> 

Re: [Owldb-users] Problem using OWLDB inside JBoss

[Jörg H. <He...@ki...>]

Hello Chowdary,

could you provide us more details about your Problem? E.g. a stacktrace when an error occurs?
Perhaps http://docs.jboss.org/jbossas/getting_started/v4/html/hibernate.html can help you withe the integration of the owldb code.
My best guess is that there are also problem with the use of JNDI and the context lookup.

greets
Joerg

Re: [Owldb-users] Problem using OWLDB inside JBoss

[Chowdary D. <dvr...@gm...>]

To be more clear, I am trying to use OWLDB in my EJB tier to store parts of
my main database which uses JPA as the persistence mechanism. So, I guess
its the problem with hibernate.cfg.xml that OWLDB uses as I already have a
persistence.xml.

On Mon, Feb 1, 2010 at 10:27 PM, Chowdary Davuluri
<dvr...@gm...>wrote:

> Hi,
> I couldn't succeed using OWLDB inside Jboss. Calling the owldb api either
> from a stateless session bean or a normal class throws me errors. What might
> the reasons be ?
>
> Thank,
> Chowdary Davuluri
>

[Owldb-users] Problem using OWLDB inside JBoss

[Chowdary D. <dvr...@gm...>]

Hi,
I couldn't succeed using OWLDB inside Jboss. Calling the owldb api either
from a stateless session bean or a normal class throws me errors. What might
the reasons be ?

Thank,
Chowdary Davuluri

[Owldb-users] Fwd: Owldb-users post from dvrmchowdhary@gmail.com requires approval

[Joachim K. <joa...@go...>]

---------- Forwarded message ----------
From: Joachim Kleb <joa...@go...>
Date: 2010/1/2
Subject: Re: [Owldb-users] Owldb-users post from
dvr...@gm... approval
To: Chowdary DVRM <dvr...@gm...>


Hi Chowdary,

The "hibernate.cfg.xml"-file is not in included in the system path.  Please
add the file to the "path"-environment variable. Select the appropriate file
included in the subfolders in the /config-folder. Means, use
/config/MySql/hibernate.cfg.xml, if you are running a mysql-database.
After that you should be able to run the program.

Best,
Joachim

2009/12/17 Chowdary DVRM <dvr...@gm...>

Hi Jaochim,
> I get the following error when I try using owldb.
> -------------------------------------------------------------
> INFO [main] (?:?) - Loading ontology: jdbc:mysql://localhost/owldb
>  INFO [main] (Environment.java:560) - Hibernate 3.3.2.GA
>  INFO [main] (Environment.java:593) - hibernate.properties not found
>  INFO [main] (Environment.java:771) - Bytecode provider name : javassist
>  INFO [main] (Environment.java:652) - using JDK 1.4 java.sql.Timestamp
> handling
>  INFO [main] (Configuration.java:1474) - configuring from resource:
> /hibernate.cfg.xml
>  INFO [main] (Configuration.java:1451) - Configuration resource:
> /hibernate.cfg.xml
> ERROR [main] (?:?) - Initial SessionFactory creation failed.
> org.hibernate.HibernateException: /hibernate.cfg.xml not found
>     at
> org.hibernate.util.ConfigHelper.getResourceAsStream(ConfigHelper.java:170)
>     at
> org.hibernate.cfg.Configuration.getConfigurationInputStream(Configuration.java:1453)
>     at org.hibernate.cfg.Configuration.configure(Configuration.java:1475)
>     at org.hibernate.cfg.Configuration.configure(Configuration.java:1462)
>     at de.fraunhofer.iitb.owldb.util.HibernateCfgUtil.<init>(Unknown
> Source)
>     at de.fraunhofer.iitb.owldb.OWLDBOntology.<init>(Unknown Source)
>     at
> de.fraunhofer.iitb.owldb.OWLDBOntologyFactory.createOWLOntology(Unknown
> Source)
>     at
> de.fraunhofer.iitb.owldb.OWLDBOntologyFactory.createOWLOntology(Unknown
> Source)
>     at de.fraunhofer.iitb.owldb.OWLDBOntologyManager.createOntology(Unknown
> Source)
>     at de.fraunhofer.iitb.owldb.OWLDBStorer.storeOntology(Unknown Source)
>     at de.fraunhofer.iitb.owldb.OWLDBStorer.storeOntology(Unknown Source)
>     at de.fraunhofer.iitb.owldb.OWLDBOntologyManager.saveOntology(Unknown
> Source)
>     at ceti.osu.test.owldb.MyOwlDBTest.storeOntology(MyOwlDBTest.java:24)
>     at ceti.osu.test.owldb.MyOwlDBTest.main(MyOwlDBTest.java:36)
> Exception in thread "main" java.lang.ExceptionInInitializerError
>     at de.fraunhofer.iitb.owldb.util.HibernateCfgUtil.<init>(Unknown
> Source)
>     at de.fraunhofer.iitb.owldb.OWLDBOntology.<init>(Unknown Source)
>     at
> de.fraunhofer.iitb.owldb.OWLDBOntologyFactory.createOWLOntology(Unknown
> Source)
>     at
> de.fraunhofer.iitb.owldb.OWLDBOntologyFactory.createOWLOntology(Unknown
> Source)
>     at de.fraunhofer.iitb.owldb.OWLDBOntologyManager.createOntology(Unknown
> Source)
>     at de.fraunhofer.iitb.owldb.OWLDBStorer.storeOntology(Unknown Source)
>     at de.fraunhofer.iitb.owldb.OWLDBStorer.storeOntology(Unknown Source)
>     at de.fraunhofer.iitb.owldb.OWLDBOntologyManager.saveOntology(Unknown
> Source)
>     at ceti.osu.test.owldb.MyOwlDBTest.storeOntology(MyOwlDBTest.java:24)
>     at ceti.osu.test.owldb.MyOwlDBTest.main(MyOwlDBTest.java:36)
> Caused by: org.hibernate.HibernateException: /hibernate.cfg.xml not found
>     at
> org.hibernate.util.ConfigHelper.getResourceAsStream(ConfigHelper.java:170)
>     at
> org.hibernate.cfg.Configuration.getConfigurationInputStream(Configuration.java:1453)
>     at org.hibernate.cfg.Configuration.configure(Configuration.java:1475)
>     at org.hibernate.cfg.Configuration.configure(Configuration.java:1462)
>     ... 10 more
> ----------------------------------------
> I am not sure which hibernate.cfg.xml is being looked for. I tried creating
> it in my project, but I still doesn't work.
>
> Thanks,
> Chowdary.
>
> On Tue, Dec 8, 2009 at 12:59 AM, Joachim Kleb <joa...@go...
> > wrote:
>
>>  Hi Chowdary,
>>
>> Sorry for the late reply. Regarding your first question: there is
>> currently no generated jar-file
>> included. The project repository include two ant-build-files in order to
>> build the project and also create the jar-files.
>> Therefore use ant (ant.apache.org) and execute "ant build" on the
>> command line.
>> 2: The java-doc will be also created during the build process. There
>> will be a folder "javadoc" including all necessary html-files.
>> There are also examples included in the source code explaining how to
>> use OWLDB.
>> 3: OWLDB make use of the OWL-API (http://owlapi.sourceforge.net/) and
>> represents a database-backend for this api. Thus you can use the
>> querying and reasoning functionality of the owl-api in order to access
>> your ontology stored via the owldb in your database.
>> OWLDB uses an hibernate-mapping that allows to map the ontology
>> represented by the owlapi in a database. Here we tried to optimise the
>> mapping regarding the general requirements of owl. The resulting schema
>> is very specific. Reusing projects with already existing database
>> schemas and transfering their data to an ontology means to map the data
>> between both worlds. That could be done either by a programm focused on
>> database transformations or by a programm reading your existing database
>> and transfering it to owlapi objects. Subsequently it would be
>> automatically stored in a database based on the owldb functionality.
>>
>> As an alternative you can also use D2R2
>> (http://www4.wiwiss.fu-berlin.de/bizer/d2rq/) in order to map your
>> existing db-schema to an ontology, dump it as rdf-ontology and use owldb
>> as database-backend for this ontology.
>>
>> Best,
>> Joachim
>>
>>
>>  ------------------------------
>>   Subject:
>> A question on OWLDB
>> From:
>> Chowdary DVRM <dvr...@gm...> <dvr...@gm...>
>> Date:
>> Fri, 4 Dec 2009 11:22:48 -0500
>> To:
>> owl...@li...
>> To:
>> owl...@li...  Hi,
>> I am trying to use OWLDB in my project and I have a few questions which I
>> request you to help me with.
>>
>> 1. I don't see a jar file of the distribution in the svn. Where can I find
>> it ?
>> 2. Where can I find the javadoc for the api ?
>> 3. I would like to know how the ontology(TBox and ABox) stored in a
>> realational DB like MySQL can be queried and loaded into a reasoner like
>> Pellet using owldb(may be going through owldb's api doc might help). In my
>> project, the ontology schema and the existing database schema are a little
>> different(with many overlappings) and I would like to query my database
>> first to populate the ontology and load it into a reasoner for inferencing
>> and store the entailments back into the database. So, basically, I guess I
>> am trying to replicate what you have done with OWLdB. It would be great if
>> you can comment on such situations where I don't want to stick to a database
>> automatically generated from an ontology schema which is what I guess owl db
>> does.
>>
>> Thanks&Regards,
>> Chowdary Davuluri,
>> M.S. in CS&E,
>> The Ohio State University.
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Join us December 9, 2009 for the Red Hat Virtual Experience,
>> a free event focused on virtualization and cloud computing.
>> Attend in-depth sessions from your desk. Your couch. Anywhere.
>> http://p.sf.net/sfu/redhat-sfdev2dev
>> _______________________________________________
>> Owldb-users mailing list
>>
>> Owl...@li...
>> https://lists.sourceforge.net/lists/listinfo/owldb-users
>>
>>
>

[Owldb-users] Fwd: Owldb-users post from dvrmchowdhary@gmail.com requires approval

[Joachim K. <joa...@go...>]

---------- Forwarded message ----------
From: Chowdary DVRM <dvr...@gm...>
Date: 2009/12/17
Subject: Re: [Owldb-users] Owldb-users post from
dvr...@gm... approval
To: Joachim Kleb <joa...@go...>


Hi Jaochim,
I get the following error when I try using owldb.
-------------------------------------------------------------
INFO [main] (?:?) - Loading ontology: jdbc:mysql://localhost/owldb
 INFO [main] (Environment.java:560) - Hibernate 3.3.2.GA
 INFO [main] (Environment.java:593) - hibernate.properties not found
 INFO [main] (Environment.java:771) - Bytecode provider name : javassist
 INFO [main] (Environment.java:652) - using JDK 1.4 java.sql.Timestamp
handling
 INFO [main] (Configuration.java:1474) - configuring from resource:
/hibernate.cfg.xml
 INFO [main] (Configuration.java:1451) - Configuration resource:
/hibernate.cfg.xml
ERROR [main] (?:?) - Initial SessionFactory creation failed.
org.hibernate.HibernateException: /hibernate.cfg.xml not found
    at
org.hibernate.util.ConfigHelper.getResourceAsStream(ConfigHelper.java:170)
    at
org.hibernate.cfg.Configuration.getConfigurationInputStream(Configuration.java:1453)
    at org.hibernate.cfg.Configuration.configure(Configuration.java:1475)
    at org.hibernate.cfg.Configuration.configure(Configuration.java:1462)
    at de.fraunhofer.iitb.owldb.util.HibernateCfgUtil.<init>(Unknown Source)
    at de.fraunhofer.iitb.owldb.OWLDBOntology.<init>(Unknown Source)
    at
de.fraunhofer.iitb.owldb.OWLDBOntologyFactory.createOWLOntology(Unknown
Source)
    at
de.fraunhofer.iitb.owldb.OWLDBOntologyFactory.createOWLOntology(Unknown
Source)
    at de.fraunhofer.iitb.owldb.OWLDBOntologyManager.createOntology(Unknown
Source)
    at de.fraunhofer.iitb.owldb.OWLDBStorer.storeOntology(Unknown Source)
    at de.fraunhofer.iitb.owldb.OWLDBStorer.storeOntology(Unknown Source)
    at de.fraunhofer.iitb.owldb.OWLDBOntologyManager.saveOntology(Unknown
Source)
    at ceti.osu.test.owldb.MyOwlDBTest.storeOntology(MyOwlDBTest.java:24)
    at ceti.osu.test.owldb.MyOwlDBTest.main(MyOwlDBTest.java:36)
Exception in thread "main" java.lang.ExceptionInInitializerError
    at de.fraunhofer.iitb.owldb.util.HibernateCfgUtil.<init>(Unknown Source)
    at de.fraunhofer.iitb.owldb.OWLDBOntology.<init>(Unknown Source)
    at
de.fraunhofer.iitb.owldb.OWLDBOntologyFactory.createOWLOntology(Unknown
Source)
    at
de.fraunhofer.iitb.owldb.OWLDBOntologyFactory.createOWLOntology(Unknown
Source)
    at de.fraunhofer.iitb.owldb.OWLDBOntologyManager.createOntology(Unknown
Source)
    at de.fraunhofer.iitb.owldb.OWLDBStorer.storeOntology(Unknown Source)
    at de.fraunhofer.iitb.owldb.OWLDBStorer.storeOntology(Unknown Source)
    at de.fraunhofer.iitb.owldb.OWLDBOntologyManager.saveOntology(Unknown
Source)
    at ceti.osu.test.owldb.MyOwlDBTest.storeOntology(MyOwlDBTest.java:24)
    at ceti.osu.test.owldb.MyOwlDBTest.main(MyOwlDBTest.java:36)
Caused by: org.hibernate.HibernateException: /hibernate.cfg.xml not found
    at
org.hibernate.util.ConfigHelper.getResourceAsStream(ConfigHelper.java:170)
    at
org.hibernate.cfg.Configuration.getConfigurationInputStream(Configuration.java:1453)
    at org.hibernate.cfg.Configuration.configure(Configuration.java:1475)
    at org.hibernate.cfg.Configuration.configure(Configuration.java:1462)
    ... 10 more
----------------------------------------
I am not sure which hibernate.cfg.xml is being looked for. I tried creating
it in my project, but I still doesn't work.

Thanks,
Chowdary.

On Tue, Dec 8, 2009 at 12:59 AM, Joachim Kleb
<joa...@go...>wrote:

>  Hi Chowdary,
>
> Sorry for the late reply. Regarding your first question: there is currently
> no generated jar-file
> included. The project repository include two ant-build-files in order to
> build the project and also create the jar-files.
> Therefore use ant (ant.apache.org) and execute "ant build" on the
> command line.
> 2: The java-doc will be also created during the build process. There
> will be a folder "javadoc" including all necessary html-files.
> There are also examples included in the source code explaining how to
> use OWLDB.
> 3: OWLDB make use of the OWL-API (http://owlapi.sourceforge.net/) and
> represents a database-backend for this api. Thus you can use the
> querying and reasoning functionality of the owl-api in order to access
> your ontology stored via the owldb in your database.
> OWLDB uses an hibernate-mapping that allows to map the ontology
> represented by the owlapi in a database. Here we tried to optimise the
> mapping regarding the general requirements of owl. The resulting schema
> is very specific. Reusing projects with already existing database
> schemas and transfering their data to an ontology means to map the data
> between both worlds. That could be done either by a programm focused on
> database transformations or by a programm reading your existing database
> and transfering it to owlapi objects. Subsequently it would be
> automatically stored in a database based on the owldb functionality.
>
> As an alternative you can also use D2R2
> (http://www4.wiwiss.fu-berlin.de/bizer/d2rq/) in order to map your
> existing db-schema to an ontology, dump it as rdf-ontology and use owldb
> as database-backend for this ontology.
>
> Best,
> Joachim
>
>
>  ------------------------------
>   Subject:
> A question on OWLDB
> From:
> Chowdary DVRM <dvr...@gm...> <dvr...@gm...>
> Date:
> Fri, 4 Dec 2009 11:22:48 -0500
> To:
> owl...@li...
> To:
> owl...@li...  Hi,
> I am trying to use OWLDB in my project and I have a few questions which I
> request you to help me with.
>
> 1. I don't see a jar file of the distribution in the svn. Where can I find
> it ?
> 2. Where can I find the javadoc for the api ?
> 3. I would like to know how the ontology(TBox and ABox) stored in a
> realational DB like MySQL can be queried and loaded into a reasoner like
> Pellet using owldb(may be going through owldb's api doc might help). In my
> project, the ontology schema and the existing database schema are a little
> different(with many overlappings) and I would like to query my database
> first to populate the ontology and load it into a reasoner for inferencing
> and store the entailments back into the database. So, basically, I guess I
> am trying to replicate what you have done with OWLdB. It would be great if
> you can comment on such situations where I don't want to stick to a database
> automatically generated from an ontology schema which is what I guess owl db
> does.
>
> Thanks&Regards,
> Chowdary Davuluri,
> M.S. in CS&E,
> The Ohio State University.
>
>
>
> ------------------------------------------------------------------------------
> Join us December 9, 2009 for the Red Hat Virtual Experience,
> a free event focused on virtualization and cloud computing.
> Attend in-depth sessions from your desk. Your couch. Anywhere.
> http://p.sf.net/sfu/redhat-sfdev2dev
> _______________________________________________
> Owldb-users mailing list
>
> Owl...@li...
> https://lists.sourceforge.net/lists/listinfo/owldb-users
>
>

Re: [Owldb-users] Owldb-users post from dvrmchowdhary@gmail.com requires approval

[Joachim K. <joa...@go...>]

Hi Chowdary,

Sorry for the late reply. Regarding your first question: there is 
currently no generated jar-file
included. The project repository include two ant-build-files in order to
build the project and also create the jar-files.
Therefore use ant (ant.apache.org) and execute "ant build" on the
command line.
2: The java-doc will be also created during the build process. There
will be a folder "javadoc" including all necessary html-files.
There are also examples included in the source code explaining how to
use OWLDB.
3: OWLDB make use of the OWL-API (http://owlapi.sourceforge.net/) and
represents a database-backend for this api. Thus you can use the
querying and reasoning functionality of the owl-api in order to access
your ontology stored via the owldb in your database.
OWLDB uses an hibernate-mapping that allows to map the ontology
represented by the owlapi in a database. Here we tried to optimise the
mapping regarding the general requirements of owl. The resulting schema
is very specific. Reusing projects with already existing database
schemas and transfering their data to an ontology means to map the data
between both worlds. That could be done either by a programm focused on
database transformations or by a programm reading your existing database
and transfering it to owlapi objects. Subsequently it would be
automatically stored in a database based on the owldb functionality.

As an alternative you can also use D2R2
(http://www4.wiwiss.fu-berlin.de/bizer/d2rq/) in order to map your
existing db-schema to an ontology, dump it as rdf-ontology and use owldb
as database-backend for this ontology.

Best,
Joachim


> ------------------------------------------------------------------------
> Subject:
> A question on OWLDB
> From:
> Chowdary DVRM <dvr...@gm...>
> Date:
> Fri, 4 Dec 2009 11:22:48 -0500
> To:
> owl...@li...
>
> To:
> owl...@li...
>
> Hi,
> I am trying to use OWLDB in my project and I have a few questions 
> which I request you to help me with.
>
> 1. I don't see a jar file of the distribution in the svn. Where can I 
> find it ?
> 2. Where can I find the javadoc for the api ?
> 3. I would like to know how the ontology(TBox and ABox) stored in a 
> realational DB like MySQL can be queried and loaded into a reasoner 
> like Pellet using owldb(may be going through owldb's api doc might 
> help). In my project, the ontology schema and the existing database 
> schema are a little different(with many overlappings) and I would like 
> to query my database first to populate the ontology and load it into a 
> reasoner for inferencing and store the entailments back into the 
> database. So, basically, I guess I am trying to replicate what you 
> have done with OWLdB. It would be great if you can comment on such 
> situations where I don't want to stick to a database automatically 
> generated from an ontology schema which is what I guess owl db does.
>
> Thanks&Regards,
> Chowdary Davuluri,
> M.S. in CS&E,
> The Ohio State University.

[Owldb-users] A question on OWLDB

[Chowdary D. <dvr...@gm...>]

Hi,
I am trying to use OWLDB in my project and I have a few questions which I
request you to help me with.

1. I don't see a jar file of the distribution in the svn. Where can I find
it ?
2. Where can I find the javadoc for the api ?
3. I would like to know how the ontology(TBox and ABox) stored in a
realational DB like MySQL can be queried and loaded into a reasoner like
Pellet using owldb(may be going through owldb's api doc might help). In my
project, the ontology schema and the existing database schema are a little
different(with many overlappings) and I would like to query my database
first to populate the ontology and load it into a reasoner for inferencing
and store the entailments back into the database. So, basically, I guess I
am trying to replicate what you have done with OWLdB. It would be great if
you can comment on such situations where I don't want to stick to a database
automatically generated from an ontology schema which is what I guess owl db
does.

Thanks&Regards,
Chowdary Davuluri,
M.S. in CS&E,
The Ohio State University.