User manual ¶

Contents

User manual

Implementation architecture ¶

Fig. 14 shows the system architecture of MR³ from the aspect of system implementation. MR³ is implemented in Java language, using the Java Swing user interface. MR³ uses JGraph for RDF(S) graph visualization, and Apache Jena for enabling the use of Semantic Web standards such as RDF, RDFS, and OWL. The Parser and Generator in MR³ are implemented using Jena APIs. By using these libraries, MR³ is implemented as an environment for graphical representation of Semantic Web descriptions. Additionally, MR³ also has a plug-in facility to extend its functionality. At present, MR³ offers two kinds of APIs for plug-in development: one for changing the MR³ data graph into a model object of Jena, and one for changing the model object of Jena into a MR³ data graph.

Fig. 14 Implementation architecture of MR³

System overview ¶

Fig. 15 shows the system overview of MR³ . MR³ consists of the Parser module, Generator module, Meta-Model Management module, Plug-ins, and User Interface. The user edits the RDFs description visually via the User Interface, which also includes the Graphical Modeler and Plug-in interfaces. The Graphical Modeler provides access to the basic functions of MR³ , while the Plug-in Interface provides access to the functions of the plug-ins. The input and output of MR³ are RDFs documents. The Parser analyzes input RDFs documents and makes further operations possible by transforming the RDFs document into a Jena model. Then, the Parser changes the Jena model into an internal data expression, and meta-model management is performed. Plug-ins are built using APIs provided by MR³ . The Generator changes the internal data expression into a Jena model. Finally, the Jena model is changed into an RDFs document.

Fig. 15 System overview of MR³

Overview of the Graphical modeler ¶

Fig. 16 shows a typical screen showing the Graphical Modeler interface of MR³ . The Graphical Modeler consists of five main windows; RDF Editor, Class Editor, Property Editor, Attribute Dialog, and Namespace Table.

The details of the graphical modeler are shown in the following sections.

Fig. 16 Typical screen with Graphical Modeler interface of MR³

RDF Editor ¶

The RDF Editor allows the user to express the relationship between an RDF resource, RDF property, and RDF literal using a directed graph, and also allows the attributes of each element to be edited. The attributes of an RDF resource consist of a URI, the URI type, and the RDF resource type. The RDF resource type can be chosen using the Class Editor. The URI type can be chosen from either a URI or can be set as anonymous.

As shown in Fig. 17, RDF resources are represented as ellipses, RDF properties are represented as arrows, and RDF literals are represented as rectangles in the RDF editor . Types of RDF resources are shown at the upper right part of the RDF resources.

Fig. 17 RDF Editor

Toolbar in the RDF Editor ¶

Icons in the toolbar in the RDF editor and the corresponding functions are shown in the following table.

Icon	Function
	Move nodes
	Connect nodes
	Select a corresponding RDFS class or property
	Don’t select a corresponding RDFS class or property
	Insert an RDF resource
	Insert an RDF literal
	Undo
	Redo
	Copy nodes
	Cut nodes
	Paste nodes
	Remov nodes
	Show resource find dialog
	Set default magnification
	Expand the RDF editor
	Reduce the RDF editor
	Set appropriate magnification
	Group nodes
	Ungroup nodes
	Automatically layout the RDF graph

Editing attributes of RDF resources ¶

When users select an RDF resource in the RDF editor, the attributes of the RDF resource are shown in the Attribute Dialog ( Fig. 20 to Fig. 27 ). The attributes of RDF resources are URI, rdf:type, blank node or note, rdfs:label, and rdfs:comment. Here the blank nodes are RDF resources that are not named by URIs. Blank nodes can not be acceced from external documents. However, the blank nodes can be subjects or objects of statements. They are used to represent RDF resources that are difficult to name or structure RDF contents.

If users would like to set a URI of an RDF resource, they should select URI from the left side menus in the Attribute Dialog as shown in Fig. 20. Prefixes that are registered in the Namespace Table are shown in The prefix combo box. When users select one of the prefixes in the combo box, the corresponding namespace is shown in the RDF Resource text field. The users can input any URI in the text field. If the users would like to set an RDF resource as a blank node, the users should check the blank checkbox.

Fig. 20 Attribute Dialog (URI of an RDF resource)

If the users would like to set a type to an RDF resource, the users should select the Type from the left side menu in the Attribute Dialog as shown in Fig. 21. The isType checkbox should be checked when the users input the type of an RDF resource. If the users would like to empty the type of an RDF resource, they should uncheck the isType checkbox.

When the users click the Select Type button, Select Resource Type Dialog are shown as shown in Fig. 22. The class hierarchy that is build in the Class editor is shown in the Select Resource Type Dialog. When the users select an RDFS class in the dialog, the namespace and ID of the selected class are set in the Attribute Dialog.

When the users input a URI that is not defined in the Class editor, RDF(S) contents management dialog is shown as shown in Fig. 23. In the RDF(S) contents management dialog, the users can select Rename or Create.

When the users click the JumpClass button, the type of an RDF resource is selected and the attributes of the type of the RDF resource are shown in the Attribute Dialog.

Fig. 21 Attribute Dialog (type of RDF resource)

Fig. 22 RDF Resource Type Selection Dialog

Fig. 23 RDF(S) contents management dialog

If the users would like to define the rdfs:label of an RDF resource, the users should select Label in the left side menu in the Attribute Dialog as shown in Fig. 24. After inputting language in the Lang text field and label in the Label text field, the language and the label are added in the table in the Attribute Dialog. If the users select a line in the table and click remove button, the selected label is removed.

Fig. 24 Attribute Dialog (Label of an RDF resource)

If the users would like to define the rdfs:comment of an RDF resource, the users should select Comment in the left side menu in the Attribute Dialog as shown in Fig. 25. After clicking the Add button, the Edit Comment Dialog is shown.

First input language in the Lang text field and comment in the Comment text area. Then, click OK button. After that, the language and the label are added in the table in the Attribute Dialog. If the users select a line in the table and click Edit button, the users can edit the selected comment and the language. In the same way, if the user select a line in the table and click Remove button, the selected label is removed.

Fig. 25 Attribute Dialog (Comment of an RDF resource)

Editing attributes of RDF properties ¶

If the users select an RDF property in the RDF Editor, the attributes of the RDF property are shown in the Attribute Dialog (Fig. 26). The users can edit the URI of the selected RDF property.

If the users check the isContainer checkbox and input a number, the users can set rdf:_1 to n property that is corresponding to the inputted number.

If the user check the Show Property Prefix Only checkbox, the users can only select prefixes that are only used in the defined RDFS properties. If the user uncheck the checkbox, the users can select all of the prefixes that are defined in the Namespace Table.

Fig. 26 Attribute Dialog (RDF Property)

When the users input a URI which is not defined in the Property Editor, RDF(S) contents management dialog is shown as shown in Fig. 23. In the RDF(S) contents management dialog, the users can select rename the RDFS property or create an RDFS property.

When the users select one of the prefixes in the dialog, IDs of RDFS properties that are defined in the Property Editor and the namespace is correspond to the selected prefix are shown in the Property ID list.

When the users select one of the Property IDs and click (Jump) Property button, the RDFS property is selected and the attributes of the RDFS property are shown in the Attribute Dialog.

Editing attributes of RDF literals ¶

When the users select an RDF literal in the RDF Editor, the attributes of the RDF literal are shown in the Attribute Dialog. (Fig. 27) The users can edit the contents of the literal, the attribute of language (xml:lang), and the data type of the literal. In the Literal text are, the users can input the contents of the literal. The users can also input language in the Lang text field. If the users set the data type of the literal, the users should check isType checkbox and select one of the types in the Type combobox. Language attribute and data type attribute are exclusive and the users only select one of them.

Fig. 27 Attribute Dialog (RDF Literal)

Class Editor ¶

The Class Editor allows the users to edit the attributes of RDFS classes and the relationships between the classes.

Fig. 28 shows an screenshot of the Class Editor

Fig. 28 An screenshot of the Class Editor

Toolbar in the Class Editor ¶

Icons in the toolbar in the Class editor and the corresponding functions are shown in the following table.

Icon	Function
	Move nodes
	Connect nodes
	Insert an RDFS class
	Undo
	Redo
	Copy nodes
	Cut nodes
	Paste nodes
	Remove nodes
	Show resource search dialog
	Set default magnification
	Expand the Class Editor
	Reduct the Class Editor
	Set appropriate magnification
	Group nodes
	Ungroup nodes
	Automatically layout the RDFS class graph

Editing attributes of the Class editor ¶

When the users select an RDFS class in the Class Editor, the attributes of the RDFS class are shown in the Attribute Dialog (Fig. 31 to Fig. 33). The users can edit the attributes of an RDFS class by selecting Base, Label, Comment, Instances, or UpperClasses items from the left side menu in the Attribute Dialog.

When the users select the Base item, the type of an RDFS class and the URI can be edited (Fig. 31). The types can be defined class class list in the Config Dialog. When the users select the Label item, the value of rdfs:label property can be edited. When the users select the Comment item, the value of rdfs:comment property can be edited. The methods for editing rdfs:label and rdfs:comment are same as RDF resource. When the users select the Instances item, the instances of the selected RDFS class are shown in the list (Fig. 32). When the users select the one of the items in the list, corresponding RDF resource is selected and the attributes of the RDF resource are shown in the Attribute Dialog. When the users select the UpperClasses item, the uppser classes of the selected RDFS class are shown in the list (Fig. 33).

Fig. 31 Attribute Dialog (Base of RDFS class)

Fig. 32 Attribute Dialog (Instances of the RDFS class)

Fig. 33 Attribute Dialog (Upper classes of the RDFS class)

Property Editor ¶

The Property Editor allows the users to edit the attributes of RDFS properties and the relationships between the properties.

Fig. 34 shows an screenshot of the Property Editor

Fig. 34 An screenshot of the Property Editor

Toolbar in the Property Editor ¶

Icons in the toolbar in the Property editor and the corresponding functions are shown in the following table.

Icon	Function
	Move nodes
	Connect nodes
	Insert an RDFS property
	Undo
	Redo
	Copy nodes
	Cut nodes
	Paste nodes
	Remove nodes
	Show Resource Search Dialog
	Set default magnification
	Expand the Property Editor
	Reduce the Property Editor
	Set appropriate magnification
	Group nodes
	Ungroup nodes
	Automatically layout the RDFS property graph

Editing attributes of the Property editor ¶

When the users select an RDFS property in the Property Editor, the attributes of the RDFS property are shown in the Attribute Dialog (Fig. 37 to Fig. 39). The users can edit the attributes of an RDFS property by selecting Base, Label, Comment, Region, Instance, or SuperProperties items in the left side menu of the Attribute Dialog. Base, Label, and Comment items are same as RDFS Class. The type list in the Base item can be defined in the property class list in the Config Dialog. When the users select Region item, domains and ranges of the selected RDFS property can be edited (Fig. 37). When the users select Instances item, RDF resource list that have the selected RDFS property is shown in the Attribute Dialog (Fig. 38). When the users select the one of the items in the list, the RDF resource is selected and the attributes of the RDF resource are shown in the Attribute Dialog. When the users select SuperProperties item, super properties of the selected RDFS property are shown in the list (Fig. 39).

Attribute Dialog (Rnage of RDFS property)

Fig. 37 Attribute Dialog (Range of RDFS property)

Fig. 38 Attribute Dialog (Instances of RDFS property)

Fig. 39 Attribute Dialog (Super properties of RDFS property)

Resource Search Dialog ¶

The users can find resources (RDF resources, RDF properties, RDFS classes, and RDFS properties) by using Resource Search Dialog. Fig. 40 shows a screenshot of the Resource Search Dialog. The users can set search scope by checking the Graph Type (RDF, Class, or Property). When the users set a URI in the URI text field, resources that partially match the URI are shown in the Find Result list in the Resource Search Dialog. When the users select the one of the items in the list, corresponding resource is selected and the attributes of the resource are shown in the Attribute Dialog. The users can set the value of rdfs:label and rdfs:comment in the Label or Comment text field.

Fig. 40 A screenshot of the Resource search dialog

Namespace Table ¶

The users can register perfixes and the corresponding namespaces in the Namespace Table. Fig. 41 shows a screenshot of the Namespace Table. When the users set a prefix in the Prefix text field, set a namespace in the NameSpace text field, and click Add button, the prefix and the namespace are added in the table in the Namespace Table. If the users would like to remove the prefix and the corresponding namespace, select the line in the table and click Remove button. If the users check the available checkbox, namespaces of resources in each editor are replaced with the corresponding prefix (This function is only available when the Display->URI menu is selected.). When the users set a URI of an resource, the Namespace Table is referred and the users can select the registered prefixes in the Attribute Dialog. When the users select one of the prefixes, the corresponding namespace is shown in the Namespace label or RDF Resource text field.

Fig. 41 A screenshot of the Namespace Table

Remove Dialog ¶

If an RDFS class is referred by a type of a resource or a domain or a range of a property, it is inconsistency when the RDFS class is removed. If an RDFS property is reffered in the RDF editor, it is inconsistency when the RDFS property is removed. In these cases, when the users remove those RDFS classes or properties, the Remove Dialog as shown in Fig. 42 is shown before removing them actually.

Removed RDFS classes or properties are shown in the upper part of Fig. 42. RDF resources that referred the removed RDFS classes as their type are shown in the RDF tab in the lower part of Fig. 42. RDF properties that referred the removed RDFS properties are also shown in the RDF tab. RDFS properties that refer removed RDFS classes as their domains or ranges are shown in the Property tab in the lower part of Fig. 42.

If the users check the Delete Checkboxes and click Apply button, RDF resources, RDF properties, and RDFS properties that listed in the lower part of the Remove Dialog stop referring to the removed RDFS classes or RDFS properties. Then, the RDFS classes and RDFS properties are actually removed.

If the users select one of the RDF resources, RDF properties, or RDFS properties, attributes of the selected resource are shown in the Attribute Dialog. Then, the users can edit the attributes to maintain consistency.

Fig. 42 Remove Dialog

Import Dialog ¶

The users can import RDF(S) documents described as RDF/XML, N3, N-Triple, or Turtle format to MR³ by using Import Dialog. Fig. 43 shows a screenshot of the Import Dialog. The parts of the Import Dialog (1 to 13 in Fig. 43) are shown below.

Fig. 43 A screenshot of the Import Dialog

Directory or URI

Directories that RDF(S) documents are saved or URIs that are RDF(S) documents are shown in the list.
Add Dir

Add a directory in the Directory or URI list.
Add URI

Add a URI in the Directory or URI list.
Remove

Remove the selected directory or URI in the Directory or URI list.
Syntax

Select a syntax (RDF/XML, N3, N-Triple, or Turtle) of an RDF(S) document that the users would like to import
Data Type

Select a data type (RDF, RDFS, or OWL) of an RDF(S) document that the users would like to import
Import Method

If the users select Merge, an RDF(S) document is merged to the current project. If the users select Replace, an RDF(S) document is replaced with the current project.
Find Resource

The files in the Import File List are filtered by inputted keyword in the Find Resource text field.
Import File List

Files in the selected directory in the Directory or URI list are shown in the Import File List.
Extension

The files in the Import File List are filtered by selected extensions.
Reload

Reload the directories in the directory or URI list and the lates files are shown in the Import File List.
Import

Import an RDF(S) document to MR³ based on the set condition (syntax, data type, import method, and import file).
Cancel

Close the Import Dialog.

Export Dialog ¶

The users can export RDF(S) data graphs in MR³ to an RDF(S) document as RDF/XML, N3, N-Triple, or Turtle syntax. Fig. 44 shows a screenshot of the Export Dialog. The parts of the Export Dialog (1 to 8 in Fig. 44) are described below.

Fig. 44 A screenshot of the Export Dialog

Syntax

Select a syntax (RDF/XML，N-Triple，Turtle，N3, etc) of an RDF(S) document that the users would like to export.
Data Type

If the users check the RDF, Class, or Property checkbox, data graphs in the selected editor are exported to an RDF(S) document. (For example, if the users checks Class and Property, classes and properties are exported as an RDF(S) document.)
Option

If the users check Encode(UTF-8) checkbox, URIs of resources are encoded based on RFC3986. If the users check Selected checkbox, only selected nodes are exported. If the users check Abbrev checkbox, data graphs are exported as RDF/XML Abbreviation syntax. If the users check XMLbase checkbox, XMLBase declaration is added in the RDF(S) document.
File

Export an RDF(S) document based on the set condition (syntax, data type, and options).
Image

If the users select one of the data types (RDF, Class, or Property) and click Image button, the selected data graph is saved as an image file.
Reload

The latest data graph are exported based on the set condition and the source is shown in the 8 part.
Cancel

Close the Export Dialog.
Show the source of RDFs models

The users can confirm the source of an RDF(S) document that will be exported.

Config Dialog ¶

The users can set configurations about basic, directory, proxy, meta class, layout, and rendering in the Config Dialog.

Basic ¶

When the users select the Basic item as shown in Fig. 45, language, UI language, output encoding, font, base URI, and log file can be set. If a resource has many multilingual labels, the users should select the prior language. The prior language of labels can be set in the Lang text field. Labels with prior language are shown in each resource when the user select display->label menu. Language of UI such as menu can be set in the UI Lang list. The users can select ja (Japanese), en (English), or zh (Chinsese) from the UI Lang list. Output encoding can be used to export an RDF(S) document. The font of resources can be set by clicking Font Setting button and selecting a font from the font selecting dialog. Default namespace is set based on the Base URI. The directory that a log file is saved can be set by clicking Browse button and selecting the directory from the directory selection dialog.

Fig. 45 Config Dialog: Basic

Directory ¶

When the users select the Directory item as shown in Fig. 46, work directory, plugins directory, and resources directory can be set. The work directory is a directory that is opened firstly when the users import an RDF(S) document. The plugins directory is a directory that plug-ins of MR³ are saved. The resources directory is a directory that property files are saved. The property files are defined labels that displayed in MR³ for each language.

Fig. 46 Config Dialog: Directory

Proxy ¶

When the users select the Proxy item as shown in Fig. 47, a host name and a port number of a proxy server can be set. This configuration is necessary to import an RDF(S) document from a URI when the user’s environment is under a proxy server.

Fig. 47 Config Dialog: Proxy

Meta Class ¶

When the users select the Meta Class item as shown in Fig. 48, Class Class and Property Class can be set. If the users set a Class Class, MR³ regards resources that have the Class Class as their type as classes. If the users set a Property Class, MR³ regards resources that have the Property Class as their type as properties. These classes and properties are imported in the RDFS class editor or RDFS property editor.

In the initial setting, rdfs:Class is defined in Class Class and rdf:Property is defined in Property Class. If the users would like to import OWL classes and properties, owl:Class must be set as Class Class, owl:ObjectProperty and owl:DatatypeProperty must be set as Property Class.

Fig. 48 Config Dialog: Meta Class

Layout ¶

When the users select the Layout item as shown in Fig. 49, methods for layout for each editor can be set.

Fig. 49 Config Dialog: Layout

Rendering ¶

When the users select Rendering item as shown in Fig. 50, colors of each node (RDF resources, RDF literals, RDFS classes, and RDFS properties), colors of each selected node, and background color of each editor can be set. If the users uncheck the Color checkbox, all of the nodes become colorless. If the users check the Antialias checkbox, an edge of each node become smooth.

Fig. 50 Config Dialog: Rendering

Plugins ¶

When the users select Plugins sub menu in the Tool menu, the dialog as shown in Fig. 51 is shown. MR³ loads jar files in the plug-ins directory that is set in the Config Dialog. The plugins are shown in the list. If the users select one of the plugins, the description of the plugin is shown at the bottom of the dialog. If the users click Exec button, the selected plugin is executed. Please refer to Plugin Development to build MR³ plugins.

Fig. 51 Plugins

Validator ¶

When the users select Validator sub menu in the Tool menu, the dialog as shown in Fig. 52 is shown. MR³ uses Apache Jena’s validation API (org.apache.jena.reasoner.ValidityReport ) and it is enabled to check if the data type of literals are defined based on a range of property.

Fig. 52 Validator

Project Info ¶

When the users select Project Info sub menu in the Tool menu, the dialog as shown in Fig. 53 is shown. The current project name, the number of RDF resources, the number of RDF literals, the number of RDF statements, the number of classes, the number of properties, the number of all resources, the number of all literals, the number of all statements are shown in the dialog.

Fig. 53 Project Info

File->New Project: Create new MR³ project. The users should select save the current project or delete it.
File->Open Project: Open MR³ project file
File->Save Project: Save MR³ project file
File->Save As Project: Save As MR³ project file
File->Import: Show Import Dialog
File->Export: Show Export Dialog
File->Exit: Exit MR³

Edit ¶

Edit->Find Resource: Show Find Resource Dialog

Edit->Select->Select All RDF Nodes

Edit->Select->Select All Class Nodes

Edit->Select->Select All Property Nodes

View ¶

View->URI View: URIs of resources are shown in each editor. If namespaces are defined in the Namespace Table, the corresponding prefixes are replaced with the namespaces.
View->ID View: IDs of resources are shown in each editor.
View->Label View: Values of rdfs:label properties are shown in each editor. If a resource does not have rdfs:label property, the URI of the resource is shown instead of the value of rdfs:label property.
View->Show Resource Type: If the users check the Show Resource Type, the type of RDF resources are shown at the top right of each resource.
View->Show RDF Property Label: If the users check the Show RDF Property Label, the label of properties are shown. If it is not checked, the label properties are not shown in the RDF editor.
View->Show ToolTips: If the users check the Show ToolTips, tooltips are shown when the users mouse over the resources.
View->Apply Layout->RDF: Automatically layout the RDF graph
View->Apply Layout->Class: Automatically layout the Class graph
View->Apply Layout->Property: Automatically layout the Property graph

Window ¶

Window->Show RDF Editor Overview: The overview of the RDF editor is shown in the dialog. When the users drag a red rectangle, part of the RDF graph in the red rectangle are shown in the RDF editor. The users can change the size of the red rectangle by dragging the right down part. It is enabled to expand and reduce the editor.
Window->Show Class Editor Overview: The overview of the Class editor is shown in the dialog. The functions of the dialog is as same as RDF Editor Overview.
Window->Show Property Editor Overview: The overview of the Property editor is shown in the dialog. The functions of the dialog is as same as RDF Editor Overview.

Window->To Front RDF Editor

Window->To Front Class Editor

Window->To Front Property Editor

Window->Show Attribute Dialog

Window->Show Namespace Table

Window->Layout->Deploy Windows (C,P,R): The RDF editor, the Property editor, and the Class editor are shown.
Window->Layout->Deploy Windows (C,R): The Class editor and the RDF editor are shown.
Window->Layout->Deploy Windows (P,R): The Property editor and the RDF editor are shown.

Help ¶

Help->About MR³: The developer, version, license, project web site, contact, and libraries used in MR³ are shown in the dialog.

Toolbar ¶

Icon	Function
	New MR³ project
	Open MR³ project file
	Save MR³ project file
	Save as MR³ project file
	Show Import Dialog
	Show Export Dialog
	Show Resource Search Dialog
	Show RDF Editor to the front
	Show Class Editor to the front
	Show Property Editor to the front
	Show Attribute Dialog to the front
	Show Namespace Table to the front
	Show Class, Property, and RDF Editors
	Show Class and RDF Editors
	Show Property and RDF Editors
	Find previous
	Find next
	Validate RDFs contents
	Show Plugin Management Dialog
	Show Project Information
	Show Log Console
	Show Config Dialog
	Show about MR³

Shortcut keys ¶

Shortcut keys that can be used in MR³ ¶

Ctrl-N: Create new MR³ project. The users should select save the current project or delete it.
Ctrl-O: Open MR³ project file
Ctrl-S: Save MR³ project file
Ctrl+Shift+S: Save as MR³ project file
Ctrl+Q: Exit MR³
Alt+R: Show the RDF Editor to the front
Alt+C: Show the Class Editor to the front
Alt+P: Show the Property Editor to the front
Alt+A: Show the Attribute Dialog
Alt+N: Show the Namespace Table
Alt+F: Show the Find Resource Dialog

Shortcut keys that can be used in editors ¶

Ctrl-A: Select all of the nodes in a editor
Delete: Delete selected nodes in a editor
Ctrl-C: Copy selected nodes in a editor
Ctrl-X: Cut selected nodes in a editor
Ctrl-V: Paste nodes that are copied or cut.