Difference between revisions of "OntoBase"

OntoBase

by Len Yabloko

OntoBase is a plug-in that connects Protege to relational databases. It allows ontologies to be used as views and forms for data entry.

Versions & Compatibility

This section lists available versions of OntoBase.

If you click on the button below to add a new version of OntoBase, you will be asked to define a page title for the new version. Please adhere to the naming convention of OntoBase X.X.X when you define the new page!

More Details

Description

OntoBase is a plug-in that turns any relational database into ontology. You can define new classes by mapping slots to columns of one or more tables. It allows Protégé to be used as "Model" and "View" for simple database applications. OntoBase can also be used as “back end” for Protégé in order to store parts of knowledge base which must be shared with other applications. In its current form OntoBase can be simply “snapped on” any relational database to provide access to data, virtually without any programming.

Installation

The ONTOBaseTab can work with "basic" or "full" installation of Protege 3.x, but it requires JDK 1.6 To make sure Protege loads with correct JVM change following line in protege.lax file

lax.nl.current.vm=C:\\Program Files\\Java\\jre1.6.0_04\\bin\\java.exe

1) Extract OntoBase_X.X.X.zip into Protege installation root directory.

2) Open New Project using Protege files(.pont and .pins) or XML file

3) Go to Project->Configure and check ONTOBaseTab box.

4) When OntoBase window appears enter JDBC address of database and click connect button.
Following are some examples of JDBC database URLs:

jdbc:oracle:thin:@machine_name:port_number:instance_name
jdbc:mysql://host_name:port/dbname 

Note: JDBC driver corresponding to entered URL must be provided either by placing it directly in Protege root directory under name driver1.jar (or driver2.jar, driver3.jar etc.), or by placing it in location specified in following line of protege.lax file

lax.class.path=protege.jar;...;dbdrivers/sqljdbc.jar; dbdrivers/ojdbc6.jar; dbdrivers/mysql-connector-java-5.1.6-bin.jar...

Drivers tested with OntoBase:

http://dev.mysql.com/downloads/connector/j/5.1.html

http://download.oracle.com/otn/utilities_drivers/jdbc/111060/lib/ojdbc6.jar

http://download.microsoft.com/download/b/4/7/b4761c5f-2d80-40dc-aa86-0795c70893e8/Download_SQL_JDBC_Driver_12.htm

5) Wait until connection is established and then click on "run" icon.

Note: If import does not start in a few moments or stops before 100%, then you may need to adjust application memory allocation by editing following line in protege.lax file

lax.nl.java.option.java.heap.size.initial=100000000

The protege.lax file is located in the root directory of your Protege installation

6) After import of database schema is finished OntoBase will re-load and check sign will appear next to imported url. At this point Protege project will contain "ground" ontology generated by OntoBase with four top level classes:

:THING
     :SYSTEM-CLASS
     .TUPLE
     ~STREAM
     @GROUND
     =SERVICE

Note: All top level classes (except ~STREAM) should have sub-classes corresponding to each table in the database.

7) To test generated "ground" ontology simply select any sub-class of =SERVICE corresponding to a table and press "create" button on OntoBase tab. You should see a class instance popup corresponding to an empty row of the table. Fill any field and close the popup: this should result in fetching corresponding row of the table (or error message will appear in OntoBase window).

8) Now you are ready to use OntoBase for defining new classes and mapping them to tables or joins. To do that simply select =SERVICE and press "create" button again. You should see a popup asking you to select a table. After selection follow next popup.

Note: OntoBase popups are regular Protege instances. Look for useful instructions in "documentation" field of each popup.

If you have any problems or questions contact support@ontospace.net