Semafora OntoStudio3 - 2 User Manual 2017
Semafora OntoStudio3 - 2 User Manual 2017
Table of Content
General
...........................................................................................................5
Installation
...........................................................................................................5
Deinstallation
...........................................................................................................6
Starting OntoStudio
...........................................................................................................8
User Interface Overview
...........................................................................................................12
Hot Keys
...........................................................................................................13
Setting Preferences
...........................................................................................................23
Adding Comments and Labels
...........................................................................................................24
Extending Functions by Extension Points
..............................................................................................25
Extension Points Overview
ExtendableTreeProvider
..............................................................................................25
ExtendableDropHandler
..............................................................................................25
EntityProperties
..............................................................................................25
..............................................................................................26
Configuring Extension Points
Schema of ExtandableTreeProvider
..............................................................................................26
Schema of ExtandableDropHandler
..............................................................................................27
Schema of EntityProperties
..............................................................................................28
Mapping..............................................................................................29
Extension Points
Schema of ontomapMappingTransformationEditor
..............................................................................................29
Schema of ontomapComplexMappingExtension
..............................................................................................30
...........................................................................................................32
BIRT (Business Intelligence and Reporting Tools)
Creating..............................................................................................32
a report with BIRT
..............................................................................................48
Deploying a report on Tomcat
..............................................................................................48
Input Parameters for BIRT
Creating a Report Displaying Author Deta
..............................................................................................50
Modeling
...........................................................................................................74
Ontology Navigator
...........................................................................................................75
Entity Properties
...........................................................................................................79
Classes
...........................................................................................................85
Instances
...........................................................................................................88
Relations
...........................................................................................................91
Validating Ontologies
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...........................................................................................................93
ObjectLogic Source Editor
...........................................................................................................94
Visualizing an Ontology
...........................................................................................................96
Graph View
...........................................................................................................98
Sharing a project
...........................................................................................................101
Querying Web Services
Handling Rules
...........................................................................................................108
Entity Properties View Overview
...........................................................................................................111
(De)activating Rules
...........................................................................................................112
Explaning Rules
...........................................................................................................114
Materializing Rules
...........................................................................................................115
Creating Rules graphically
...........................................................................................................124
Debugging Rules
..............................................................................................126
Rule Graph
..............................................................................................127
Rule Literals
Tuples..............................................................................................129
Debug..............................................................................................129
Monitor
Handling Queries
...........................................................................................................130
Creating and executing a Query
...........................................................................................................131
Editing a Query
...........................................................................................................132
Editing Options of a Query
...........................................................................................................133
Displaying Results of Queries
...........................................................................................................134
Copying Rules
...........................................................................................................135
Writing ObjectLogic Queries against modelled Ontologies
...........................................................................................................137
Running a Regression Test
...........................................................................................................143
Optimizing Queries
..............................................................................................145
Optimization Methods Overview
Importing Ontologies
...........................................................................................................151
Importing from Filesystem
...........................................................................................................156
Importing from WebDAV Repository
..............................................................................................162
Editing/deleting a WebDAV Connection
...........................................................................................................162
Importing from Database Schema
..............................................................................................163
Importing a Database Schema
Editing..............................................................................................167
a database connection
Adding..............................................................................................167
new schemas and tables
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..............................................................................................168
Installing a JDBC-Driver
..............................................................................................168
Importing Oracle RDF
...........................................................................................................170
Importing from FileSystem Metadata
...........................................................................................................174
Importing from Outlook
...........................................................................................................177
Importing from Remote OntoBroker
...........................................................................................................181
Importing from UML Diagram
..............................................................................................184
Visualizing an Ontology Using UML
Exporting Ontologies
...........................................................................................................188
Exporting to Filesystem
...........................................................................................................192
Exporting to WebDAV Repository
...........................................................................................................197
Exporting to UML Diagram
Integration
...........................................................................................................202
Mapping Ontologies
...........................................................................................................211
Integrating an Excel Data Sheet
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1 General
1.1 Installation
Precondition:
You must have the rights to read and to write to your current home directory and the installation directory
because OntoStudio must access these directories e.g. for writing log files.
1. Double click on the installation ".exe file" for Windows and Linux.
2. Start OntoStudio32 (32 bit version) or OntoStudio64 (64 bit version).
The installation process starts.
3. The installation wizard guides you through the further installation.
At the end of the installation you are asked for the Key File.
4. Choose the Key File and then click on Open.
5. If you want to increase the main memory of the OntoStudio Java process, open the OntoStudio.ini file in
the installation folder of OntoStudio in a text editor and replace the -Xmx256m option with a higher
number (for example -Xmx512m to reserve up to 512 MB of RAM for OntoStudio).
For more information on the installation see the README.TXT file.
To find the complete list of OntoStudio plug-ins, select Help->About OntoStudio -> Installation Details -> Plug-
ins.
To integrate your own developed built-ins, take a look at the OntoBroker documentation or contact the support
team.
The default file format for all ontologies is ObjectLogic! For RDF & OWL this means:
Imported files that have a native format are transformed and stored as .obl in the workspace.
OWL-in-OBL are used to store (supported) OWL specific axioms.
The ObjectLogicEditor can be activated for all ontology languages.
1.2 Deinstallation
Precondition:
The Uninstall function deletes the Installation folder of OntoStudio. Make sure that you have copied the
KeyFile to another location before starting the Uninstall function; otherwise the KeyFile might be deleted!
1. From the Windows Start menu select: Start -> All Programs -> OntoStudio Version -> Uninstall.
Remove OntoStudio with the help of the uninstall wizard.
2. Click on Next.
The uninstall wizard guides you through the further uninstall process.
3. Click on Uninstall.
All of the OntoStudio components are removed.
4. Click on Accept.
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5. Click on OK.
The deinstallation starts.
6. Click on Close.
The deinstallation is finished and the OntoStudio software is not on your computer anymore. The window
closes.
OntoStudio launches.
2. Select a Workspace and then click on OK.
On starting the program for the first time, the "Workspace Launcher" dialog pops up.
3. Specify where your workspace directory is located. To create a workspace in another directory click on
Browse... and select the desired directory.
All of the information about your ontologies, your preference settings, and so on is stored in the workspace
directory.
NOTE: The restoring of old workspaces is not supported. As a workaround the projects have to be
re-created and the ontologies have to be re-imported from the old workspace.
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3. The program starts and the start screen appears. The Modeling View appears by default.
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1 Navigation tree
2 Tool bar
Tool Bar
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4 Search function
Modeling View
All of the properties of an element selected in the navigation tree can be edited in the modeling view.
The editable information is often divided into a set of property pages which can be accessed using tabs at the
bottom of the modeling view:
Menu Bar
Use the menu bar to access the main features of Onto Studio, which include e.g. the import and export
functions, creating new ontologies or opening different perspectives, to name but a few.
Most of the menu items are default items of the Eclipse framework which are also described in the
Eclipse documentation at eclipse.org.
File Menu
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The file menu contains the standard operations of the program. Some operations are only highlighted in the
special use cases.
Search Menu
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Using OntoStudio's search function, you can run a search on classes, properties, relations and instances in
your workspace or in a set of your projects. The result of your search is displayed in the results view.
Window Menu
The Window menu offers you different ways of quickly switching between the different views of OntoStudio.
Help Menu
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The Help menu offers you an easy way to get the basic information about OntoStudio, it's version number and
the plug-in details.
F5 Refresh
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2. Browse through the Preferences dialog pages by looking through all of the titles in the left pane or
searching a smaller set of titles using the filter field at the top of the left pane.
The results returned by the filter match both Preference page titles and keywords such as "Template" or
"Data" (just examples).
Most of the settings are quite self-explanatory, so only the most important settings are described below.
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General
The General options are self-explanatory. For more information on the standard Eclipse preferences (General
Settings), see the Eclipse documentation at eclipse.org.
Graph Generation
You can specify different configuration parameters (margins and directories) for printing a graph with the
Graphviz tool.
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Language Preferences
Here you can specify the languages for which you want to develop your ontology. The chosen languages are
shown on the user interface for Adding Comments and Labels.
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Large Ontologies
If there are ontologies with so many classes or instances on the same level that scrolling would take a lot of
time, you can group them to simplify the view.
For example: 10 entities should b e grouped:
1. In the entry field Number of Entities to be grouped type in the number 10.
2. Click on Apply and then on OK.
3. Select an element (for example, a class) with more than 10 subclasses in the tree menu of the
OntologyNavigator.
The following warning message appears:
3. Click on OK.
The entities are displayed in the following format: [Subclass1,.......SubclassN]-(Number of
entities to be grouped). A new icon notifies you that the elements are grouped.
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The procedure to group instances is the same like the one described above.
You can also choose a set of classes which should only be displayed. This can be seen as a kind of filter
Mapping Preferences
As you might get a large number of facts within your mapping scenario we recommend that you define the
maximum number of fetched instances and the values that are shown in the preview. This improves the
performance of the mapping components.
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ObjectLogic Editor
It shows the content of an ontology as ObjectLogic in a text editor. Specify whether you want to use the syntax
highlighting (recommended) and whether you will have to set a check mark (confirm dialog) when opening an
ontology in the ObjectLogic editor.
Use the Colors and Templates options to set the appearance of the ObjectLogic textual editor.
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Query Tool
By default, the queries you create and run in OntoStudio are executed against the embedded OntoBroker. If
you have an OntoBroker instance running somewhere, you can also use OntoStudio to send queries to the
running OntoBroker. To do this you only have to select the "External Server" option and then provide the
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connection details.
NOTE: Queries against the external OntoBroker should be fully qualified. If you select the "External
Server" option, all OntoStudio queries are sent to the external server. If you want to run queries on your
local ontologies again, you have to switch back to the "Internal Server" mode.
Report Design
These preferences are equal to standard BIRT preferences. The documentation of the BIRT report plug-ins
can be found at the BIRT project page (http://www.eclipse.org/birt/).
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Validator
Here you can specify sets of constraints (which are displayed in the Constraint sets frame). The different
constraints of the selected constraint set are displayed in the Constraints frame.
To create a new set of constraints, click on Add... next to the Constraint sets frame. Choose a name for the
new set and click on OK. You can see the new set in the Constraint sets frame.
To add a constraint to a set, select the name of the set and click on Add... next to the Constraints frame. Use
the newly opened window to write the description of the constraint in the Description frame and the constraint
itself in the Constraints frame. Then click on OK and you see the new constraint in the Constraints frame.
You can delete or edit a created constraint/set of constraints by selecting it and clicking on Delete or Edit...
respectively.
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Visualizer
This view displays the ontology and all of the hierarchy elements (classes, relations, properties, instances) in
a graph. As your ontology might have a large number of Properties, it is better not to set the checkmarks.
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1. To add a translation to a term, click in the relevant field in the column Label and enter the translation.
2. To add a description, click in the relevant field in the column Comment and enter the description in the
yellow text entry field.
3. To add further languages, select Window -> Preferences -> Lanugages Preferences, select a new
language in the drop down box Create new locale... and click on Create.
4. To reorder the languages, select Window -> Preferences -> Lanugages Preferences, select a language
and click on Up or Down.
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1.8.1.2 ExtendableDropHandler
With the org.neontoolkit.gui.extandableTreeProviderextandableDropHandler extension-point you
can define additional drag&drop operations on the OntologyNavigator using the org.neontoolkit.gui.
extendableDropHandler extension-point. Two kinds of drag&drop operations are possible:
object-type-specific drag&drop
transfer-type-specific drag&drop
In the case of the object-type-specific drag&drop, you can define which class will handle drops from objects of
a specific type A on objects on a second specified type B. These object-type-specific drag&drop operations
only work within the application with components using the com.ontoprise.ontostudio.gui.navigator.
SelectionTransfer transfer type.
The transfer-type-specific drag&drop also works between different applications as well as between plugins
within the application. For this kind of drag&drop the class used for the transfer operation is used to determine
the class handling the drag&drop operation. Therefore, the developer can, for example, define a new transfer
class and then register his own handler for this type of transfer on the OntologyNavigator.
1.8.1.3 EntityProperties
The org.neontoolkit.gui.entityProperties extension point gives you the option of integrating new
property pages in the Entity Properties View. Therefore the org.neontoolkit.gui.entityProperties
extension point has to be extended. In this extension point you can define for which types of elements selected
in the user interface the property page should be shown.
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id - a unique identifier used to reference the component which should display the contents of this
extension.
The interface of ITreeDataProvider must be implemented and provides the following methods:
Method Descripton
ITreeElement[] getElements(ITreeElement This method should return the given amount of root
parentElement, int topIndex, int amount) elements of this provider beginning at index topIndex.
The passed parentElement is an element of the
parent provider or null if none
Image getImage(ITreeElement element) Should return the image of the tree element (which
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Method Descripton
String getText(ITreeElement element) Should return the text of the tree element (which was
provided by this provider) to be displayed in the UI.
void setId(String id) Sets the identifier of this provider. This method is
invoked from the framework to set the id specified in
the plugin.xml.
void setViewer(ComplexTreeViewer viewer) Passes the reference to the TreeViewer that displays
the content of this provider. The reference is used to
perform refresh operations
boolean isDragSupported() The developer can define the general behavior of the
elements provided by this provider. If true is returned,
the elements can generally be dragged, if a handler
for this kind of drag is registered. If false is returned,
these elements cannot be dragged at all.
boolean isDropSupported() The developer can define the general drop policy on
elements provided by this provider. If true is returned,
it is possible to drop elements on the elements of
this provider (if a dropHandler is registered for this
kind of drop). If false is returned, these elements do
not support any drop operation at all.
<!ELEMENT dropHandler>
<!ATTLIST dropHandler
class CDATA #REQUIRED
dragClass CDATA #REQUIRED
dropClass CDATA #REQUIRED>
class - the fully qualified name of the class that implements org.eclipse.swt.dnd.
DropTargetListener.
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<!ELEMENT transferHandler>
<!ATTLIST transferHandler
class CDATA #REQUIRED
transferClass CDATA #REQUIRED
class - the fully qualified name of the class that implements org.eclipse.swt.dnd.
DropTargetListener.
transferClass - The class name of the transfer type this DropTarget listener is associated with.
For both types of drag&drop handling, the interface to implement is the org.eclipse.swt.dnd.
DropTargetListener interface. The description of this interface can be found in the SWT documentation.
<!ELEMENT entityPropertyContributor(subContributorOf?)>
<!ATTLIST entityPropertyContributor
id CDATA #IMPLIED
class CDATA #REQUIRED
name CDATA #REQUIRED
activatorClass CDATA #IMPLIED>
<!ELEMENT subContributorOf>
<!ATTLIST subContributorOf
superContributorId CDATA #REQUIRED
priority CDATA #IMPLIED
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Composite createContents(Composite parent); This method is invoked, when the property page is
created. The parent component is passed as argument and the child component should be created
in this method and returned afterwards
void deSelect(); This method is called if a different property page is about to show because another
element has been selected. Clean up operations can be done in this method.
Image getImage(); Should return the image to display in the header of the Entity Properties View if
the property page is shown.
boolean isDisposed(); Should return true if the property page is disposed or false otherwise.
void refresh(); Is called if a refresh of the user interface of the property page is needed.
void refreshData(); Is called if the data model has changed and a refresh of the displayed
information in the property page is needed
void setSelection(IWorkbench part, IStructuredSelection selection); Is called by the framework to
pass the current selection to the associated property page.
There is already an abstract implementation of this page for ontology elements. This class is named com.
ontoprise.ontostudio.gui.properties.BasicEntityPropertyPage. It already provides editing areas for identifiers
and namespaces as well as optional documentation and representation fields.
ontomapComplexMappingExtension
To plug-in special implementations for certain mapping-patterns an extension of the com.ontoprise.
ontostudio.ontomap.ontomapComplexMappingExtension extension-point can be used for
implementing the com.ontoprise.ontostudio.ontomap.mapping.provider.IMappingProvider
interface. The implementation of the IMappingProvider is responsible for collecting all of the
information needed for the mapping and the rule creation. It has to provide the gui for the initial creation
and the editing of mappings for this pattern type as well as storing the mapping meta-data. An
implementation of com.ontoprise.ontostudio.ontomap.control.mapping.IMappingInstance or
alternatively com.ontoprise.ontostudio.ontomap.control.mapping.AbstractMappingInstance
is responsible for the mapping rule generation.
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editorClass - The fully qualified name of the class that implements com.ontoprise.ontostudio.
ontomap.views.IMappingTransformationEditor.
editorName - The name of the transformation editor.
category - The category of the transformation editor
The interface of IMappingTransformationEditor must be implemented and provides the following methods:
Method Description
void init(IMapping mapping) This method initializes the GUI components for the
mapping transformation editor for the given mapping.
void init(IMapping mapping, FormToolkit toolkit) This method initializes the GUI components for the
mapping transformation editor for the given mapping.
void addUpdateFormListener(IPropertyFormListener Allows to inform the parent GUI component that a GUI
l) update is needed.
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mappingProviderClass - the fully qualified name of the class that implements com.ontoprise.
ontostudio.ontomap.mapping.provider.IMappingProvider.
name - The name of the mappingProvider.
The interface of IMappingProvider must be implemented and provides the following methods:
Method Description
boolean matches(INode[] sourceNodes, INode[] Returns true if the mapping pattern is applicable for
targetNodes) the given user selection within the mapping view.
boolean canSaveMapping() Returns true if all data needed for the mapping
creation is available.
boolean supportsMapping(IMapping mapping) Returns true if the MappingProvider supports the type
of the given mapping.
void init(INode[] sourceNodes, INode[] targetNodes This method initializes the GUI components for the
mapping pattern based on the given mapping nodes.
void init(IMapping mapping) This method initializes the GUI components for the
mapping properties based on the given mapping.
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Method Description
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b. Select OntoBroker Data Source and give a name to the data source and click on Next.
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c. Choose the query for which the report will be created and click on Finish.
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d. Click on OK.
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9. Drag&Drop the data set element from the Data Explorer to the new report view to create a simple table
view of your data.
See below for the result:
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16. Drag&drop the data column to the appropriate text field and click on Next.
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2. Create a Report.
a. Make a right mouse click on a project and select New -> Report.
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A dialog appears.
b. Select OntoBroker Data Source and give a name to the Data Source and click on Next.
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c. Select the project, the module and the query queryProjects and click on Finish.
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d. In the left hand menu, click on Computed Columns and then click on New....
A new dialog appears:
e. Enter a name and a data type, and click on the symbol fx.
A new dialog appears:
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f. Write a formula containing the forename and last name. Click on OK.
The formula has been added to the Expression field.
The "replace" function has been used to delete the quotes which are displayed as a default and hence
give a better display.
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g. Click on OK.
The new column has been created.
h. Click on OK.
The data set has been created.
5. Make a right mouse click on Report Parameters and select New Parameter:
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A dialog appears.
6. Fill out the different fields in the following way and click on OK:
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c. Select the project, the module and the query queryProjectsDetails. Click on Finish.
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f. In the Direction field select Input from the drop-down list. In the Linked to report parameter field,
select ProjectsList from the drop-down list.
An input parameter is defined in order to restrict the query.
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g. Click on OK.
The second data set is created.
9. Drag&Drop this second data set from the Data Explorer tab to the report.
A table is displayed in the report:
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10. Click on the Preview tab and on the Show Report Parameters button.
A dialog box appears:
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2 Modeling
You can create and maintain semantic models (often referred to as "ontologies") written in the ObjectLogic,
RDF and OWL languages. Due to a harmonization of ObjectLogic, OWL and RDF to help make OntoStudio
more user friendly, OntoStudio now provides one single perspective for all three ontology languages. The
modeling perspective is the only and the easiest way to modify your ontologies. Its simple and user friendly
interface is mostly self-explanatory. For more information about supported RDF and OWL features see the
README.TXT file.
An ontology defines a common vocabulary for researchers and experts who need to share information in a
domain. It includes machine-interpretable definitions of basic classes in the domain and relations between
them.
Why would someone want to develop an ontology?
To share common understanding of the structure of information among people.
To enable the reuse of the domain and expert knowledge.
To make the domain assumptions explicit.
To separate the domain and expert knowledge from the operational knowledge.
To analyze the domain and expert knowledge.
Furthermore, you must answer the following questions when developing an ontology:
Which domain will the ontology cover?
What is the purpose of the ontology?
To what types of questions should the information in the ontology provide answers?
Who will use and maintain the ontology?
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You can navigate within the hierarchically arranged elements. Each project can contain several ontologies. For
each ontology, classes can be found in the classes folder, properties in the properties folder, and so on.
Furthermore, you can create, change and delete ontology elements. The different options for editing the
elements are listed in the appropriate context menu. To open the context menu of an element, make a right
mouse click on the element. If an element contains further sub-elements, then a plus sign is displayed on the
left side of the element. Click on this plus sign to display the sub-elements. To close the view of the sub-
elements, click on the minus sign next to the upper element.
Ontology Details
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Namespaces
A list of defined namespaces with their aliases is displayed. You can add, remove or edit the namespaces
and aliases. The default display in the Ontology Navigator and in the Entity Properties pages does not contain
the elements' namespace. You can display it by selecting Show URI, as presented below:
Moreover, you can display the alias by selecting Show QName. The result is:
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It is possible to create new entities using namespace aliases. For example, the classes of the same ontology
can have different namespaces:
Ontology Imports
OntoStudio provides a functionality for importing facts from other ontology projects. You can enhance these
facts on your own but you can't edit them much.The import function section describes how to import
ontologies. In the screenshot below, on the Ontology Imports tab of the Entity properties view, you can see
that "ontowebtravel" is the imported ontology, which has been imported into the "genealogy" ontology. You can
add several ontologies to the imports of an ontology. By flagging the Show elements of imported ontologies
checkbox, all facts of the imported ontology will be displayed grey-shaded in the Ontology Navigator, like the
classes "Customer", "Date" an "Location".
You can neither modify the imported entities, nor delete them. But you can of course add new elements like
classes, properties, instances, etc. Imported rules are also valid in the importing ontology.
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2.3 Classes
When you select a class in the navigator tree an Entity Property is displayed. This chapter describes the tabs
of the Entity Properties view.
Properties
You can edit all properties of an element selected in the navigator tree in the Entity Properties view:
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NOTE: Additional information about the three mostly used attribute values:
String is the simplest value type which is used for properties such as name. The value is a simple string.
Double: (There exist different numerical value types, such as float or integer) describes properties with
numeric values.
Boolean: properties are simple true/false flags.
Properties can have parameters. The syntax for writing parameters is the following:
name(param1, param2,...) with "name" being the name of the relation or attribute
"param1", "param2"... the ranges of the different parameters
the parameters can have different ranges: either data types (string, integer, boolean...) or classes
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Synonyms
In this tab you can define synonyms in different languages for the selected element. The languages that are
displayed here can be configured in the preferences of OntoStudio. If you import old files containing synonyms
without language assignment, they are displayed in an additional table called "Without language information".
You can of course also use this table to enter synonyms without language assignment, like in the older
OntoStudio versions.
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Meta Information
2.4 Instances
When you select a class all its instances are displayed in the Instances view:
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instance will be displayed, with a randomly generated name, e.g.: instance1106663037379, which can be
changed by the user.
Instances can be easily moved by dragging them to another class or by selecting Refactor>Move from the
context menu.
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If you are editing a relation, click on CTRL+SPACE and a list of the available instances will be displayed. You
can add the proposed instances of the Value column either by double-clicking on them or selecting them with
the arrow keys on your keyboard and pressing Enter. If you start typing in the cell, the available instances will
be filtered.
If you want to edit an attribute, just select the Value cell and type in the attribute value. Click on OK to save the
modified or added values.
Cardinalities
If the property value was modeled with the cardinality 1, then the Value table will contain only one row, so only
one value can be stored. If the cardinality is anything greater than 1, you can enter as many values as like. The
exact amount will not be checked.
Datatypes
When you try to enter a value with the wrong data type (for example, you try to enter letters whereas the data
type of the attribute is "number"), a message with the problem will be displayed and nothing will be written in
the field.
If you have to enter a value for an attribute of the "dateTime" type, a message with help instructions will appear
next to the field:
You can see that there are three possibilities of writing a dateTime value:
<year>-<month>-<day>T<hour>:<minute>:<second>, e.g. 1820-04-25T12:30:00
<year>-<month>-<day>T<hour>:<minute>:<second>+<hour>:<minute>, e.g. 1820-04-25T12:30:00
+03:15
<year>-<month>-<day>T<hour>:<minute>:<second>-<hour>:<minute>, e.g. 1820-04-25T12:30:00-
03:15
In case of the two last ones, the "+<hour>:<minute>" and "-<hour>:<minute>" represent the time zone.
Modifications
In order to modify the entered value, you can either delete it with the red cross in the Value table and enter a
new one or click on this value and modify it directly in the field. When you click on OK, the old value will be
replaced by the new one.
If an instance contains values for a property that is not defined in the schema, the values will be displayed with
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an error icon. If you try to modify them a warning message will be displayed, informing that this attribute does
not exist anymore and the values cannot be modified.
This can happen if you remove a relation/attribute and don't set the checkmark that instance values should be
deleted as well.
2.5 Relations
When you select a relation in the navigator tree, the Entity Properties are displayed. This chapter described the
corresponding tabs of the Entity Properties View.
Domains & Ranges: Domain and Range define the classes connected by this relation. You can enter new
class in the Domain column. Min and Max define the cardinalities of the relation. The last two columns (
symmetric and transitive) define whether the relation is symmetric or transitive. The red cross deletes the
relation between the two classes but not the relation itself. Only if the last row is deleted in the table, the
relation is removed completely.
Inverse Relations:The Inverse column lists the relations that are inverse to the active relation.
NOTE: Additional Information about inverse relations:
In mathematical words, the relations r1 and r2 are inverse if we can conclude from A r1 B that B r2 A and vice
versa. For example, if a person A is a parent of person B, than we can conclude that person B is a child of
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person A and vice versa. So the relations "is parent of" and "is child of" are inverse to each other.
OWL Properties
RDF Properties
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3. To navigate to the entity that is not valid, click on the name in the Identifier column while pressing CTRL.
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The editor provides syntax highlighting or syntax errors warnings. The Outline displays the entities contained
in the currently edited ontology.
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1. Select Visualize Ontology from the context menu of an ontology element or select Show in Visualizer
from the context menu for a class element.
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The ontology and all elements of the hierarchy (classes, properties) are displayed in a graph. Classes,
instances and inheritance hierarchy are displayed in a directed graph. Properties are displayed in a directed
graph. A zoom function and a rotate function are available. The layout of the graph is optimized automatically.
Left-clicking on an element in the Ontology Visualizer will refresh the visualization rendering and the clicked
element will become its centre.
The colours of the arrows of graph elements have the following meaning:
Grey arrows: Represent the connection between superclasses and subclasses or between a superclass
and an ontology root.
Orange arrows: Represent the connection between classes and properties.
Red arrows: Represent the connection between classes and relations.
2. To append all of the connections of an element to the current visualization without shifting the focus to
this element, right-click on an element.
3. To enable or disable different ontology entities, flag the appropriate check boxes in the legend which is
on the left hand side of the view.
4. To zoom in or out, you have the following alternatives:
Change the zoom value in the selection box or
Press "Ctrl & +" to zoom in and "Ctrl & -" to zoom out.
Use the mouse wheel while holding Ctrl pressed
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In the Setting Window you can select different templates to visualize the graph diagram.
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You can export the generated graph as a pdf document, a png image or use the print function.
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3. Enter the project name and select Collaboration Server as the Storage Type. Then click on Next.
The following dialog box appears:
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If you select your collaboration project, the project properties will be shown in the Entity Properties. In the
Users section you will see a list of all users which are currently logged in on the collaboration server. If you
select your collaboration project, the Edit... button on the property page will allow you to change the connection
settings. A dialog will appear in which in which you can change the connection data of the collaboration server.
If you select an ontology, you will see the users that are currently working on the ontology in the Users section
of the property page.
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1. Select a query in the Ontology Navigator and make a right click on it.
2. Select Web Services and Create and Test WebService in External Browser.
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4. Click on query.
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When a query is deployed as a Web service a check is made to see if there are services deployed from other
projects. In that case those services are removed via deleteDynamicSvc command (you will be asked for
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confirmation). For more information on Web services, see the OntoBroker documentation.
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3 Handling Rules
Rule Diagram
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There are four possible ways of creating a class in the Graphical Rule Editor:
Using drag and drop. Use drag and drop to drag classes into the Rule Diagram. The class will appear in
the Entity Property window.
Using the Context menu. Make a right mouse click anywhere in the Rule Diagram to display a context
menu. Then select Add Class (see above).
Using the Tooltip menu. Move the cursor across the Rule diagram to activate the tooltip menu, then click
on the Class icon (Add Class).
Using the Palette menu. Click on Class in the Palette menu, then make a left click on the Rule Diagram.
ObjectLogic Source
In this tab you can see the textual ObjectLogic representation of your rule:
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You can edit your rule in a textual editor. To open this editor, click on Textual Edit..., which is in the bottom right
hand corner of the ObjectLogic Source tab.
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2. To (re)activate the rule right click on the rule/rule folder and select Activate Rule.
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2. If you want to display all of the variables and instances used in the rule, click on the icon template.
Variables in the explanation that do not occur in the rule are highlighted in the text:
2. In the Explanation Editor write an explanation (natural language text) for the rule.
The text is stored when this editor loses the focus (i.e. when another component is activated).
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On the right there is a list of all of the (Unused) Body Variables and Instances used in the rule. These are the
same variables used in the Graphical Rule Editor.
3. If you want to add a variable or an instance of the list to your explanation, double click on an entry. Make
sure you add a blank before and after every occurrence of a variable, otherwise they will not be recognized
as such.
The variable/instance is added at the the current cursor position in the text and disappears from the list.
The created explanation is used within the query evaluation in explanation mode.
A dialog appears.
2. Select the rules you want to materialize.
If you flag the Remove rules after materialization checkbox, all of the selected rules will be removed after the
materialization.
3. Click on Finish.
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The selected rules are evaluated and the results are stored in the ontology.
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2. Add a Relation.
There are three possible ways of adding a relation.
Using a right click mouse
By clicking on a name
By choosing the relation name from the auto complete list
Proceed as follows:
a. Add relation node to class (from palette).
b. Choose a relation name.
c. Connect relation to another class.
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Aggregations Sample
For more information, see the OntoBroker Enterprise Manual (chapter "Aggregations").
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Built-ins Example
For more information see the OntoBroker Enterprise Manual (chapter Appendix -> Built-ins).
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If you select a rule part in the Rule Literals view, the Reference Explorer will show the rules that can evaluate
such a part:
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3.6.3 Tuples
This view displays the results of the selected rule.
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4 Handling Queries
OR:
In the Ontology Navigator make a right mouse click on Queries, choose New Query...
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The name of the query, the project name and the module are shown in the upper part of the Results tab. The
number of results is also displayed here.
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In the right hand corner you can find this tool bar:
This has the following functions:
When you click on the arrow of symbol 3, the results pages are listed in the following way:
These results pages are ordered and numbered from the most recent (index "[1]") to the oldest (with the
highest index; here "[6]"). The results page currently displayed is marked with the symbol at the beginning
of the line.
It is possible to select a single row or multiple rows in the results.
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It's possible to copy/move tests and folders via drag and drop (only in the same project).
5. Select/execute a test.
The Entity Properties Page for this test is displayed in the main area of OntoStudio. The page contains the
query and the expected result set:
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6. The regression tests can now be run at any time. If at least one test or test folder is selected, you can
choose Run tests from the context menu.
All selected tests are evaluated and compared against the stored information. If a folder is selected, all of the
tests in the folder will be run.
The information about the correctness of the executed tests is shown in the Regression Test View. Here you
can see how many tests have been run, how many of them completed successfully and how many have
failed.
Sometimes when the model has changed, the results may differ from the results stored in the test case.
In that case, you have the possibility to accept the returned results by clicking on Accept at the bottom of
the page. The current results will then be stored as the expected results for the test case.
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7. To show the property page for the test which already contains the query text, select the test that has been
run.
8. To run the test again, click on Rerun test .
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Genetic Optimizer
Genetic algorithms (GAs) are evolutionary algorithms that use the principle of natural selection to develop a
set of solutions towards the optimum solution. GAs are not only quite powerful, but they are also very easy to
use as most of the work can be encapsulated into a single component. It would be necessary to define a
fitness function that determines how "good" a particular solution is in comparison with others. For more
information, see the OntoBroker Enterprise Manual.
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Folder and Save as: Here you can select the file name and the directory where an optimized query will be
saved.
Restrictions: If the Timeout option is activated you can insert a timeout. When this time expires the
optimization results will be shown, otherwise the timeout is deactivated
Optimization method: Here you can select the optimization method, execution time or memory
Additional information about the Genetic Optimizer:
Consider the following query: ?- p(?X)@_defaultModule AND _unify(?X,"a").
These facts are within the edb: p(a).\n p(b).\n [...] p(z).\n
If you calculate this query from left to right, you will first have to get all 26 facts, throwing away 25 of them after
the joining AND.
Now consider this query: ?- _unify(?X,"a") AND p(?X)@_defaultModule.
If evaluated from left to right, you just have to get the fact p(a), as the value of the variable X is bound to a.
Swapping the rules might speed up the evaluations.
There might be some cases where these heuristics fail. The genetic optimizer is a tool which guesses the
permutations of rules and evaluates them afterwards. The shorter the time compared with the other queries,
the bigger the chances that parts of this rule will be taken as blueprints for the next generation of rules. As the
search space is very big, this is very time-consuming.
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This scenario is for structures of queries that just exchange their constants and where the ontology stays
stable. If you optimize it for a query for my ancestors, it should also match a query asking for your ancestors. In
a way, it is a kind of an alternative for materializing parts of the ontology.
Where it should not be used:
Queries that have very short running times or ontologies that are often changed (as after each change it
could be necessary to run optimization again), ontologies with no defined query structure, where most
queries are used just once.
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5 Importing Ontologies
OntoStudio provides many wizards that import ontologies from the file system and WebDAV, as well as
several wizards for importing ontology schemas from a couple of data sources into your ontology project. For
example, Outlook files, databases, remote running instances of OntoBroker, UML files, and files system meta
data, to name just a few. The import wizards are available under File -> Import (in the top level menu).
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3. Click on Next.
The following window appears:
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4. Click on Browse... to choose the location of the ontology you want to import.
A new window appears.
5. Select the file containing the ontology.
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6. Click on Open.
The From File... field of the Import Wizard are filled out.
7. Click on Finish.
After the import process has finished, your ontology is now available and ready to use.
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3. Click on Next.
The following dialog box appears:
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6. Check the Create a new connection to a WebDAV site box and then click on Next.
The following form appears:
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9. Select the file containing the ontology and then click on Finish.
The ontology is imported.
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NOTE: The Refresh button allows the import of a changed schema by refreshing the database cache, where
all the database schema information (table, column, primary keys, and so on) are cached.
5. Wait.
The connection with the database is being established.
6. Select the tables and the table columns to be imported and click on Next.
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NOTE: You can choose which column will be taken as ID for the instances. If the table already has a Primary
Key, the column will be automatically preselected. In this case you do not have to change it. But if no column is
preselected and you do not select at least one, then all of them will be taken as IDs which may lead to
performance problems (see the warning below). If you click on No, all of the columns will be taken as IDs. If
you click on Yes, you will be able to select one or several IDs for your instances.
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2. Create an Oracle RDF Network (Oracle 10g) or a semantic data network (Oracle 11g):
Oracle 10g:
EXECUTE SDO_RDF.CREATE_RDF_NETWORK('rdftblspace');
Oracle 11g:
EXECUTE SEM_APIS.CREATE_SEM_NETWORK('rdftblspace');
3. Create a table for RDF Data (the column with data type SDO_RDF_TRIPLE_S will be used for RDF Data):
CREATE TABLE rdftblname(id NUMBER, triple SDO_RDF_TRIPLE_S);
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Classes:
INSERT INTO rdftblname VALUES (1,
sdo_rdf_triple_s ('modelname','http://a.b.c/Concept1',
'http://www.w3.org/1999/02/22-rdf-syntax-
ns#type','http://www.w3.org/2000/01/rdf-schema#Class'));
Directsub_/3:
INSERT INTO rdftblname VALUES (3,
sdo_rdf_triple_s ('modelname','http://a.b.c/Concept3',
'http://www.w3.org/2000/01/rdf-schema#subClassOf','http://a.b.c/Concept1'));
Directatttype_/6:
INSERT INTO rdftblname VALUES (5,
sdo_rdf_triple_s ('modelname','http://a.b.c/relation1',
'http://www.w3.org/1999/02/22-rdf-syntax-
ns#type','http://www.w3.org/1999/02/22-rdf-syntax-ns#Property'));
Directisa_/3:
INSERT INTO rdftblname VALUES (8,
sdo_rdf_triple_s ('modelname','http://a.b.c/instance1',
'http://www.w3.org/1999/02/22-rdf-syntax-ns#type','http://a.b.c/Concept1'));
Representation_/4:
INSERT INTO rdftblname VALUES (9,
sdo_rdf_triple_s ('modelname','http://a.b.c/Concept1',
'http://www.w3.org/2000/01/rdf-schema#label','"testlabel"'));
Documentation_/4:
INSERT INTO rdftblname VALUES (10,
sdo_rdf_triple_s ('modelname','http://a.b.c/Concept1',
'http://www.w3.org/2000/01/rdf-schema#comment','docu'));
Att_/4:
INSERT INTO rdftblname VALUES (11,
sdo_rdf_triple_s ('modelname','http://a.b.c/instance1',
'http://a.b.c/relation1','instvalue1'));
You can find the full Oracle RDF Documentation with examples on the Oracle Home Page:
Oracle 10g: http://download-uk.oracle.com/docs/cd/B19306_01/appdev.102/b19307/sdo_rdf_concepts.
htm#CIHDIBDE
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OntoConfig Settings
To use the Oracle RDF Import with OntoStudio, set the OntoConfig parameters to the following:
ConceptNamesGround = off
useQueriesOnly = on
To use the Oracle RDF access in OntoBroker:
ConceptNamesGround = off
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3. Select the data you want to import and then click on Next.
Only the selected data are imported.
The following form appears:
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All of the selected objects were imported as instances of the classes to File or Folder.
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3. Select the data you want to import, open MS Outlook and then click on Next.
Only the selected data are imported.
The following form appears:
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5. Click on Yes to make sure that the import wizard can access your Outlook data sets.
The imported ontology is visible in the Ontology Navigator:
NOTE: Unlike the other import functions, the Outlook Import does not establish a connection to its source data
during runtime but imports all of the data from Outlook during the import process.
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5. Click on Finish.
The ontology is imported to the Ontology Navigator.
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NOTE: If the ontology is too big to show on the drawing area, none of the classes will be loaded (a warning
message appears) and you don't have to perform the following four steps:
a. Move the mouse cursor onto the drawing area and press the left mouse button.
b. Choose “Control + A” on the keyboard.
c. Make a right mouse click and choose “Delete From Diagram”.
d. Confirm the appearing dialog.
The classes of the ontology are now removed.
5. Via drag and drop it is now possible to arrange only the appropriate classes of the ontology.
This way you can create an individual view of the classes.
a. Choose a class from Outline and pull it to the drawing area.
You can also arrange the classes with the mouse.
Repeat these steps until you have the desired graphical overview of your ontology.
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Miscellaneous
1. To adjust the format of the drawing area, make a right click on the drawing area without a choosing a
class and choose Graphical Properties -> Change Diagram Properties.
2. To change the layout of the classes and properties, select a class or a property from the drawing area.
3. To change the visibility of certain elements of a class or property, select Graphics in the tab Properties in
the lower part and use the buttons Hide > and < Show.
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6 Exporting Ontologies
The export function provides wizards for saving your ontologies in different file formats such as ObjectLogic,
OXML, UML, OWL or RDF(S).
Rules, queries and mappings are not supported by owl and rdf(s) and will not be exported. Furthermore,
cardinalities and also symmetric, inverse and transitive relations are not supported by the rdf(s)-export and
will also not be exported.
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4. Choose the target directory, a name and a format for the file and click on Save.
The empty field in the export wizard is filled out:
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5. Click on Finish.
The ontology is exported.
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You have to specify where you want to export the ontology to.
3. Choose a project, select an ontology and click on Settings....
The following form appears:
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3. Choose a project, an ontology and click on Browse... to specify the destination the ontology is exported to.
The following form appears:
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4. Choose the target directory and a name for the exported ontology and click on Save.
The empty field in the export wizard is filled out:
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5. Click on Finish.
The ontology is exported.
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7 Integration
Mappings can be specified based on graphical representation, using a schema-view of the respective
ontologies. You just have to understand the semantics of the graphical representation (e.g. an arrow
connecting two classes), you do not have to worry about the logical representation of mappings. You are
supported with the help of drag-and-drop functionality and simple consistency checks on property-mappings
(automatic suggestion of necessary class-mappings).
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Precondition:
1. Drag&Drop your source ontology to the top left-hand box of the Mapping window:
The class hierarchy of the ontology appears in this top left-hand box:
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When selecting a class its properties are shown within the class detail tree.
2. Drag&Drop your target ontology to the top right-hand box of the Mapping window.
The class hierarchy of the ontology appears in this top right-hand box.
3. Drag&Drop a class from the source ontology (left-hand side) onto a class from the target ontology (right-
hand side):
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suggested. When choosing a template the system guides you through the mapping definition process. In this
process you can fill out all of the necessary parameters needed for creating the mapping.
4. You can create a filter within the mapping pane: Fill out the fields in the Filters pane and click on Add:
Only instances matching the given filter criteria are returned as results.
An icon visualizes that a filter has been created:
5. Drag&Drop the properties to be mapped from the source to the target property.
You see an arrow between the mapped properties:
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6. Define a transformation.
For property mappings it is possible to define functional transformations during the mapping process.
Therefore a transformation editor for the actual selected property mappings can be chosen within the
mapping pane.
a. In the Transformations pane select a transformation type and click on Next.
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Relation-Shortcut-Pattern:
The 'Relation-Shortcut-Pattern' maps two source classes with related intermediate classes to two target
classes related directly.
For example, within the target ontology ‘analyst’ has a direct relation ‘worksinProject’ to the class
‘Project’ whereas the relation between ‘analyst' and ‘Project’ in the source ontology is expressed by an
intermediate class ‘takepartTeam’.
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Source:
Target:
Attribute-To-Relation-Instance-Pattern:
The 'Attribute-To-Relation-Instance-Pattern' maps an attribute value to a relation by creating an instance
of the target relation range with a corresponding attribute value.
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For example, the values for the source attribute ‘Project_releasedate’ are mapped as instances of
‘Project’ and values of the target attribute ‘type’ and the relation ‘hasReleaseDate’ for the target class
‘Project’.
7. To display the instances of the selected class within the Instances area, click on the Link Instances with
class tree button or on the Refresh Instances button.
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3. Click on the Open Spreadsheet icon, which is in the right hand corner of the view:
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6. Select a section (SHIFT + mouse click) of the Excel data and click on Annotate selection.
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7. Flag the Selection includes column-headers and the Annotate all available rows checkboxes.
Selection includes column-headers prevents the headers being displayed in your result.
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Annotate all available rows is useful for including all of the rows in your result instead of just the
selected ones.
9. Select the properties for each column and then click on Finish.
The annotated instances are marked.
10. Create a query on the corresponding class with the annotated properties selected and then click on Run
Query....
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OntoStudio User Manual
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care and making extensive technical checks, we cannot guarantee absolute accuracy, or completely correct
contents. No responsibility will be taken for technical errors and incorrect information or for their
consequences, e.g. effects on other programs. We are grateful to be informed of any errors at any time.
The information in this document reflects the level of information available at the time of going to press. Any
necessary corrections will be covered by subsequent versions.
semafora systems GmbH does not accept any responsibility or liability for changes caused by circumstances for
which they are not responsible.
We will accept no liability for problems with the Application Time Tracking caused by incorrect usage or for
any complications caused by third-party software.
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