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[protege-owl] Storing ontologies.

James Wiley james.wiley at
Tue Sep 12 14:34:05 PDT 2006

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 
> <mailto:Jeffrey.A.Schmitz at>> 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:
>     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
>     Get and install the MySQL JDBC driver from:
>     <>
>     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:
> <>
>     Other good sources of JENA/SPARQL Docs include:
>     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
>     <mailto:marisa.osantos at>]
>     Sent: Sun 9/3/2006 9:07 AM
>     To: 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.
>     _______________________________________________
>     protege-owl mailing list
>     protege-owl at <mailto:protege-owl at>
>     <>
> -- 
> 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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> protege-owl mailing list
> protege-owl at

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