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[protege-owl] Fwd: Storing ontologies.

Julia Dmitrieva jdmitrie at liacs.nl
Thu Sep 14 02:02:12 PDT 2006


Hello Marisa.

You have to add all jars to the classpath from
Protege_3.2_beta/plugins/edu.stanford.smi.protegex.owl.
There is also jena.jar inside.
You can take a look to plugins/edu.stanford.smi.protegex.owl,
you will see Jena.jar there.
You don't need to install Jena to work with Protege-OWL.

Protege-OWL API is build on basis of jena.
I am not an expert in Protege, but a Protege-OWL
uses all or may be part of Jena functionalities,
such as OWL model loading, saving, database, queries (SPARQL).
I am not completely sure about reasoning and rules
functionalities, because developers use Jess for rules
and RacerPro, Fact++ or Pellet for reasoning in Protege.
But Jena has also its own rules and reasoning engines.

To be honest, I am doubting self what to chose, Jena or
Protege-OWL API.
May be is there somebody who can explain what are the
advantages of Protege-OWL above Jena. I mean advantages
for developer of tools for working with ontologies, not
plugins for Protege project self.

Julia

Marisa Santos Amaro wrote:
> Sorry for my beginner´s  doubts, but I´m not sure about the right role
> of each component of this work environment for ontologies. 
> Are the statements below right or wrong ? 
> a) Protege OWL-API works with some definitions of Jena API, which are 
> already embebed in it;
> b) For loading, saving and querying OWL ontologies I can use Protege 
> OWL-API without installing
> Jena API modules;
> c) Do Jena API and Protege-OWL have the same purpose: load, 
> save and query OWL ontologies ?
> If this statement is right, when should I use each one ?
>  
> Thank you very much.
> Marisa.
>  
>  
> 
> ---------- Forwarded message ----------
> From: *Marisa Santos Amaro* <marisa.osantos at gmail.com 
> <mailto:marisa.osantos at gmail.com>>
> Date: Sep 13, 2006 5:08 PM
> Subject: Re: [protege-owl] Storing ontologies.
> To: User support for the Protege-OWL editor 
> <protege-owl at lists.stanford.edu <mailto:protege-owl at lists.stanford.edu>>
> 
>  
> Jeffrey and Wiley:
> After checking the jar files you recommended me, I removed them and 
> added again.
> I haven´t any Jena folders, because I don´t install Jena yet. 
> Now,  I´m  getting the following error messages: 
>  
> On running:
> Exception in thread "main" java.lang.Error: Unresolved compilation problem:
> OWLNamedClass cannot be resolved to a type at OWLDemo.main(OWLDemo.java:14)
>  
> Eclipse Console:
> *OWLNamedClass cannot be resolved to a type.*
> *The declared package "com.demo.application" does not match the expected 
> package.*
>  
>  
> How could I set the compiler output path in order to put my classes in 
>  Proteg "plugin/classes" folder,
> as says the Protege OWL-API Programmer´s Guide ? 
>  
> On 9/12/06, *James Wiley* <james.wiley at adelphia.net 
> <mailto:james.wiley at adelphia.net>> wrote:
> 
>     You should make sure to also add protege.jar, looks.jar,
>     unicode_panel.jar and lax.jar which is in the Protege_3.2_beta
>     directory. Setting it as your home directory won't automatically put
>     them in your build path.
> 
>     Marisa Santos Amaro wrote:
>>  Ok, Jeffrey.
>>  Before using MySQL and Jena, I´m trying to run some basic examples in
>>  the Protege-OWL API programmer´s guide, but I don´t know how to
>>  configure the Eclipse classpath (I´ve installed Protege 3.2, Eclipse
>>  3.2 and Java2SDK 1.5.08).
>>  At the "installation & getting started" section, the guide says "add
>>  all jars files from the installation to your project classpath".
>>  As my project home, I selected the "Protege_3.2_beta" directory and I
>>  created a "Demo" folder where I put the Java class from the
>>  "HelloWorld" example code. For "add jars", I selected
>>  *project>> properties>>Java buid path>>Libraries>>add external JARs*
>>  and
>>  selected the jar files from " edu.stanford.smi.protegex.owl" and
>>  "edu.stanford.smi.protegex.standard_extensions" folders to add.
>>  It didn´t work; I got 2 running error messages
>>  >> "the project was not buit since its buid path is incomplete..."and
>>  >> "the type edu.stanford.smi.protege.model.DefaultKnowledgeBase
>>  cannot be resolved. It´s indirectly referenced ...."
>>  What is wrong with this setup ?
>>  Thank you.
>>  On 9/8/06, *Schmitz, Jeffrey A* < Jeffrey.A.Schmitz at boeing.com
>     <mailto:Jeffrey.A.Schmitz at boeing.com>
>>  <mailto: Jeffrey.A.Schmitz at boeing.com
>     <mailto:Jeffrey.A.Schmitz at boeing.com>>> wrote:
>>
>>     First you will need to get everything installed on your machine.
>>     For that, here are some notes I took down from my experience. Once
>>     things are setup as below, you'll need to start coding using the
>>     JENA api. I can send you some samples of that if you want, but
>>     first things first. Note that I'm using the JENA JDBC Database
>>     option, not the Protege Database option. To get the Protege model
>>     into the JENA Database you will read in the Protege OWL file and
>>     then add that to the JENA Database Model.
>>
>>     Also, in this case it is not one table=one class but one
>>     ontology=one class. All the classes in an Ontology will be loaded
>>     into a single table (see below). If you have two Ontologies, each
>>     will get it's own table. A frequent usage is to put your Ontology
>>     class defintion in one Ontology/table, and your Instance Ontology
>>     in another.
>>
>>     Jeff
>>
>>     Get and install Mysql from:
>>
>>     http://www.mysql.com <http://www.mysql.com/>
>>
>>     You will then need to create a database and a MySQL user account
>>     in MySQL.
>>
>>     For example, start the MySQL Command Line Client application (or
>>     log into MySQL as the root user from the terminal).
>>     Enter the following commands to create the Pizza database and
>>     Pizza user:
>>
>>     mysql> CREATE DATABASE Pizzas;
>>     mysql> CREATE USER PizzaMan at localhost;
>>     mysql> SET PASSWORD FOR PizzaMan at localhost = password('pizzaPW');
>>     mysql> GRANT ALL PRIVILEGES ON *.* TO PizzaMan at localhost WITH
>>     GRANT OPTION;
>>
>>     Get and install the MySQL JDBC driver from:
>>
>>     http://dev.mysql.com/downloads/connector/j/5.0.html
>>     < http://dev.mysql.com/downloads/connector/j/5.0.html
>     <http://dev.mysql.com/downloads/connector/j/5.0.html>>
>>
>>     For Eclipse installation:
>>
>>     1. Add the JDBC Driver's jar into the build's build path, perhaps
>>     as an external jar from the Tomcat directory above, or copy it to
>>     your workspace project in Eclips and add it:
>>
>>
>>     For Protégé installation:
>>
>>     1. Rename the drive jar file to driver.jar and copy to the protégé
>>     installation folder.
>>
>>     Get and install JENA from:
>>
>>     http://jena.sourceforge.net <http://jena.sourceforge.net/> <
>     http://jena.sourceforge.net <http://jena.sourceforge.net/>>
>>
>>     Other good sources of JENA/SPARQL Docs include:
>>     http://jena.sourceforge.net/ARQ/documentation.html
>>     http://www-128.ibm.com/developerworks/xml/library/j-jena/
>     <http://www-128.ibm.com/developerworks/xml/library/j-jena/>
>>     http://www-128.ibm.com/developerworks/library/j-sparql/
>>
>>     For Eclipse Installation:
>>
>>     If you're going to develop in eclipse, make sure and add the jars
>>     to your eclipse build path.
>>
>>     Run from Eclipse:
>>
>>     Now you can develop and run your Eclipse/Jena/MySQL application
>>     from Eclipse. To check database tables manually, log on to the
>>     mysql server. For example, to login as PizzaMan:
>>
>>     Shell> mysql –u PizzaMan at localhost –ppizzaPW
>>
>>     Then select the database being used in your application. For
>>     example to use the Pizzas database:
>>
>>     Mysql> use Pizzas;
>>
>>     Then query the database tables for the information. For example:
>>
>>     Mysql> show tables;
>>
>>     You should see (for example) the Jena tables created in your
>     database:
>>
>>     jena_g1t0_reif
>>     jena_g1t1_stmt
>>     jena_g2t0_reif
>>     jena_g2t1_stmt
>>     jena_graph
>>     jena_long_lit
>>     jena_long_uri
>>     jena_prefix
>>     jena_sys_stmt
>>
>>     To look at specific OWL statements, query one of the …stmt tables;
>>
>>     Mysql> select * from jena_g1t1_stmt;
>>
>>
>>     -----Original Message-----
>>     From: Marisa Santos Amaro [mailto: marisa.osantos at gmail.com
>     <mailto:marisa.osantos at gmail.com>
>>     <mailto: marisa.osantos at gmail.com
>     <mailto:marisa.osantos at gmail.com>>]
>>     Sent: Sun 9/3/2006 9:07 AM
>>     To: protege-owl at lists.Stanford.EDU
>     <mailto:protege-owl at lists.Stanford.EDU>
>>     <mailto: protege-owl at lists.Stanford.EDU
>     <mailto:protege-owl at lists.Stanford.EDU>>
>>     Subject: [protege-owl] Storing ontologies.
>>
>>     Hi people.
>>     Does anyone know a "step-by-step" guide that I could use to learn
>>     how to
>>     store an OWL ontology in a MySQL database ?
>>     As a beginner, I have some basic doubts :
>>     a) After building the ontology, I would like to query it using an
>>     application to read the classes definitions, properties and
>     instances,
>>     because using the Protege resources I coudn´t get all mixed
>     searches I
>>     need. What kind of environment is more suitable for this goal :
>     does
>>     people usually access the ontology as a owl file (with yours
>     instances
>>     saved embedded in the code) or does it work with a backend
>>     database? The
>>     instances usually
>>     b) By reading the Protege2000 "saving a database project" section I
>>     understood that an OWL ontology can be stored as a single table.
>>     One table
>>     represents only one class, right ? So, how to save all the
>>     ontology classes
>>     ? Do I need to repeat a save-project operation for each class of
>>     my model
>>     ? And how about the instances, where/how are they saved ?
>>
>>     Where could I get good examples about these topics ?
>>
>>     Thanks a lot for any help.
>>     Marisa.
>>
>>
>>     _______________________________________________
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>>     protege-owl at lists.stanford.edu
>     <mailto:protege-owl at lists.stanford.edu> <mailto:
>     protege-owl at lists.stanford.edu <mailto:protege-owl at lists.stanford.edu>>
>>     https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>     < https://mailman.stanford.edu/mailman/listinfo/protege-owl
>     <https://mailman.stanford.edu/mailman/listinfo/protege-owl>>
>>
>>
>>
>>
>>
>>  --
>>  Marisa de Oliveira Santos Amaro
>>  Capitão-de-Fragata ( T )
>>  Superintendente de Infra-estrutura e
>>  Serviços de Tecnologia da Informação
>>  Diretoria de Finanças da Marinha - DFM
>>
>     ------------------------------------------------------------------------
>>
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>>
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> 
> 
> 
> 
> -- 
>       Marisa de Oliveira Santos Amaro
>              Capitão-de-Fragata ( T )
>      Superintendente de Infra-estrutura e
>    Serviços de Tecnologia da Informação
> Diretoria de Finanças da Marinha - DFM
> 
> 
> -- 
>       Marisa de Oliveira Santos Amaro
>              Capitão-de-Fragata ( T )
>      Superintendente de Infra-estrutura e
>    Serviços de Tecnologia da Informação
> Diretoria de Finanças da Marinha - DFM
> 
> 
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> 
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-- 
Julia Dmitrieva

LIACS Office:  124
Phone:  +31 (0)71 – 5275777
E-Mail:  jdmitrie at liacs.nl

Member of:  Imaging
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