Oracle® Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2
February 2016
Provides usage and reference information about Oracle Database support for semantic technologies, including storage, inference, and query capabilities for data and ontologies based on Resource Description Framework (RDF), RDF Schema (RDFS), and Web Ontology Language (OWL).
Introduction ...... 4 Installing and Configuring Support for Cytoscape ...... 4 Connecting to Oracle Database and Viewing a Model or Entailment ...... 9 Overview of Graph Visualization Operations ...... 12 Menu Overview ...... 12 Quick Tour: A FAMILY Social Network ...... 13 Schema Operations ...... 16 Node and Property Operations ...... 17 Search for a Concept ...... 19 Instance Summary ...... 20 Visualizing a Subset of a Graph ...... 20 Analyzing the Paths Between Nodes ...... 25 Recalculating Label Counts ...... 27 Color settings ...... 29 Data Set Sizes ...... 31 Effect of OVERLAY Option on the Displayed Graph ...... 32 Adjusting The Edge Size, Shape And Background Colors ...... 32 Construct Queries ...... 34 Shortcuts for the Most Used Features ...... 35 Saving the Steps that Created the Current View ...... 36
Oracle Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2 2
This document is an addendum to the Oracle Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1. Oracle Spatial and Graph RDF Semantic Graph Developer's Guide provides usage and reference information about Oracle Database Enterprise Edition support for semantic technologies, including storage, inference, and query capabilities for data and ontologies based on Resource Description Framework (RDF), RDF Schema (RDFS), and Web Ontology Language (OWL). The RDF Semantic Graph feature is licensed with the Oracle Spatial and Graph option to Oracle Database Enterprise Edition, and it requires the Oracle Partitioning option to Oracle Database Enterprise Edition.
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Oracle Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2 3
Introduction
Cytoscape 3.2 (also referred to here as Cytoscape) is an open source graph visualization tool. The Cytoscape Consortium describes it as a general platform for complex network analysis and visualization.
Oracle gratefully acknowledges the Cytoscape Consortium licensor of Cytoscape, which is available at http://www.cytoscape.org/download.php
Oracle Spatial and Graph RDF Semantic Graph support for Cytoscape 3.2 (also referred to here as support for Cytoscape) allows users to visualize World Wide Web Consortium (W3C) Resource Description Framework (RDF) graphs stored in Oracle Database with Cytoscape. The support for Cytoscape implements a Cytoscape “App” that conforms to the Cytoscape Apps (formerly called plugins) architecture, as described in the Cytoscape 3.0 App Development documentation.
Large RDF data sets can be stored in Oracle Database and viewed efficiently using the support for Cytoscape as subsets, summaries and samples.
• Subsets create static and dynamic views of a portion of a graph or subgraph. • Summaries capture the essence of RDF data being viewed. Summarized data can be expanded on demand, letting you create hybrid (summary-detail) fisheye views of RDF data. • Sampling creates a representative sample of the RDF data to further optimize visualization of a large dataset.
RDF data elements are stored as subject-predicate-object “triples” where the predicate expresses a relationship between the subject and the object. Triples can be asserted and inferred. Applying rules to the asserted triples using W3C standard rule sets, including the RDF Schema (RDF/S) and the Web Ontology Language (OWL) semantics, generates inferred triples. The support for Cytoscape can visualize both RDF asserted and inferred triples.
This document assumes you are familiar with the concepts, terms and information in the Oracle Spatial and Graph documentation, the RDF Semantic Graph Developer’s Guide.
Installing and Configuring Support for Cytoscape Prerequisites to install support for Cytoscape:
Oracle Database 12c Release 1, 12.1.0.1 or higher. Cytoscape 3.2.0 available from: http://www.cytoscape.org/download.html Java 7 and higher available from: https://www.java.com/en/download/
To install support for Cytoscape follow these steps.
1. Use the Cytoscape App Manager or a file copy operation to copy oraclerdf.jar into the required path
1. Use the Cytoscape App Manager:
Oracle Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2 4
1. Navigate to Apps then AppManager 2. Choose the option “Install from File” as shown in Figure 1 below. 3. Select the support for Cytoscape file, oraclerdf.jar. This option copies the file oraclerdf.jar into the path “C:\Users\[local_username]\CytoscapeConfiguration\3\apps\install ed where [local_username] refers to the current username in the operating system. 4. Start Cytoscape 3.2
2. Perform a file copy operation to move oraclerdf.jar into the path C:\Users\[local_username]\CytoscapeConfiguration\3\apps\installed, where [local_username] refers to the current username in the operating system.
Note: The directory CytoscapeConfiguration\3\apps\installed is created the first time you open Cytoscape.
Note: Please enable either oraclerdf.jar or propertyGraphSupport.jar. Do not enable both at the same time; this will avoid the confusion of two menus. Cytoscape provides an option to uninstall or disable applications from the Apps Manager. If both jars are enabled, please disable one of them to avoid errors.
2. Copy ojdbc7.jar into the Cytoscape installation path as follows: 1. Microsoft Windows: the usual location is C:\\Program Files\Cytoscape_v3.2.0\framework\lib 2. MAC OS: /Applications/Cytoscape_v3.2.0/framework/lib. 3. Linux: Cytoscape_v3.2.0/framework/lib
Oracle Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2 5
Figure 1. The application manager used to install support for Cytoscape
3. Cytoscape3.props is used to configure default values in the support for Cytoscape. This file is located in the Cytoscape configuration directory as follows: Microsoft Windows C:/Users/local_username/CytoscapeConfiguration/cytoscape3.props MAC OS and Linux: located in the user's home directory.
The following table describes the parameters that can be customized with support for Cytoscape.
Property name Description Possible values oracle-plugin.host The host to connect to Oracle Database oracle-plugin.sid The SID of Oracle Database to connect oracle-plugin.port The port to connect to Oracle Database oracle- The timeout in seconds An integer value (default value is plugin.timeout.in.seconds customized for the Oracle 30) Database connection oracle-plugin.username The username to connect to Oracle Database
Oracle Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2 6 oracle- The background color of the A hexadecimal value plugin.background.color views representing a color in the format #FFFFFF oracle- The background color of the A hexadecimal value plugin.background.color.fa views for the facets representing a color in the format cets #FFFFFF oracle-plugin.edge.type The types of possible edges {"Separate Arrow", "Contiguous Arrow", "Solid Edge", "Solid Without Arrowhead"} oracle-plugin.edge.size The width of the edge {1,2,3,4,5} the default value is 3 oracle- If true then the nodes are {true, false} plugin.use.rectangular.nod represented as rectangular nodes, es if false then nodes are represented as shapes oracle- If true then literals are included {true, false} plugin.add.literals.to.gra into the graph as nodes linked by ph edges oracle- If true then animation is used {true, false} plugin.enable.animation when nodes are expanded oracle- The value representing a A background color in a plugin.background.color.rd background color in a hexadecimal representation. For b2rdf hexadecimal format instance #DADADA oracle- If true then logging capabilities {true, false} plugin.enable.logging are enabled to log information.
Note: for security reasons, the connection password must to be provided each time a new schema connection is established.
4. Connect to Oracle Database as a user with database administrator privileges and create two new indexes using the flexible indexing scheme, as follows:
EXECUTE sem_apis.add_sem_index('SPCGM'); EXECUTE sem_apis.add_sem_index('CSPGM');
5. Rebuild the Subject-Predicate-Canonical Object-Graph-Model (SPCGM) and Canonical object- Predicate-Subject-Predicate-Graph-Model (CSPGM) indexes for any existing models that you want to visualize using Cytoscape with the following commands:
EXEC sem_apis.alter_sem_index_on_model('
Oracle Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2 7
6. It is also recommended that you rebuild the indexes for each entailment you plan to visualize.
EXECUTE SEM_APIS.ALTER_SEM_INDEX_ON_ENTAILMENT('
7. Go to the directory containing the catsemviz.sql, semviz_setup.sql and semviz.plb files.
8. Connect to Oracle Database as user SYS with SYSDBA privileges.
9. Load the catsemviz.sql file, as follows:
@catsemviz.sql
This will set up the required database tables and PLSQL packages needed for the visualization. Note: For a multitenant environment, run installation scripts using catcon.pl: $ORACLE_HOME/perl/bin/perl $ORACLE_HOME/rdbms/admin/catcon.pl -u SYS -d /home/oracle/oracle_support_12.1.0.2_for_cytoscape_3_2/PLSQL -b catsemviz_output catsemviz.sql
10. Create summaries and auxiliary data structures to optimize visualization. To do this, connect to Oracle Database as the user that owns the schema contains the RDF model(s) and enter the following statements, where
Repeat this step for every combination of model and rulebase you wish to visualize.
--Computes Class instance and Class property summary to optimize performance DECLARE cnt1 NUMBER; cnt2 NUMBER; BEGIN MDSYS.SEM_ANALYSIS.GEN_SUMMARY('
--Computes local RDF term values for fast lookup EXECUTE MDSYS.SEM_ANALYSIS.GEN_AUX_VALUES('
EXEC dbms_stats.gather_table_stats(ownname => '
Oracle Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2 8
Note: These summaries can also be created, deleted and updated graphically from the model settings panel shown in Figure 4.
Connecting to Oracle Database and Viewing a Model or Entailment Before visualizing an RDF graph stored in Oracle Database, you must have support for Cytoscape installed. After invoking Cytoscape, connect to Oracle Database, read an RDF graph or entailment (a model) into Cytoscape and explore the data. Invoking Cytoscape For Microsoft Windows: Invoke Cytoscape either by executing the shortcut provided in the Windows Start menu or executing the file cytoscape.bat located in the Cytoscape installation directory C:/Program Files/Cytoscape_v3.2
For Linux: Invoke Cytoscape by executing the script cytoscape.sh.
Connecting to Oracle Database from Cytoscape Select the option Load Data From Oracle Database from the File menu option as shown in Figure 2. Loading data from Oracle
Figure 2. Loading data from Oracle Database
A dialog box will be displayed asking for the JDBC connection settings: host, port, and database SID, driver mode, and username and password. The values in the cytoscape3.props file are displayed as the defaults. The JDBC connection string is created according to these values. Clicking on the edit button next to the text field can also customize it. This dialog is shown in Figure 3.
Oracle Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2 9
Once you have established a JDBC connection with Oracle Database by pressing the Connect button, the models available in the Oracle Database RDF graph store will be displayed as shown in Figure 3.
Figure 3. JDBC connection settings
The support for Cytoscape also supports connections using operating system authentication. In order to use this feature follow the steps below:
1. Populate the username and password fields. Click on the Connect button to be connected to Oracle Database using operating system authentication.
2. Make sure the operating system user has been created appropriately on the database server. For example, if the user is user1 the remote operating system user should be created as ops$user1. Also, while connected to the database as the user which owns the semantic model, grant the following privileges to the remote user: • grant select on mdsys.semm_
3. If the user has generated summary, demographics information on the model (recommended), then also grant the following: • grant select on mdsys.semm_psum_
Oracle Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2 10
Figure 4. The model settings panel to select an available model and rule base.
(See the RDF Semantic Graph Developer’s Guide for details about rulebases.) The Overlay option controls whether subsequent views are displayed in the current window or in a new one.
The model settings panel shown in Figure 4 is used to select an available model. Once a model has been selected, the settings are shown, including the summaries created for this model.
Note: Support for Cytoscape does not require summaries. However, it is recommended that summaries be created to enhance performance on large graphs. Some features, such as searches will not work if the summaries or the full text index have not been created. These summaries can be created, deleted or updated on demand in the model settings panel shown in Figure 4.
Pre-computed summaries replace portions of the graph with summarized data. Summaries are useful for graphs that have multiple inbound and/or outbound edges of the same predicate type for a node. Summaries help by storing a count for the number of edges of a given node and predicate combination, rather than storing each triple individually. These aggregate edges can be expanded as needed. Edge counts are not updated automatically. See the Recalculate Label Counts section.
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Viewing a Model or Entailment The root classes in the schema of the data set are initially selected and displayed for viewing and browsing. You can expand the root nodes to find an area of interest. In addition, you can expand the graph using the options described below. The resulting graph can be included in the current display or displayed in a new window by turning the OVERLAY feature on or off, respectively.
Overview of Graph Visualization Operations Figure 5 shows the basic operations allowed by the support for Cytoscape.
Figure 5. Basic Operations Overview
Regarding the operations described in Figure 5: The SPARQL-like SEM_MATCH (with focal point) capability visualizes the result of a SEM_MATCH query in Oracle Database that is centered on a node of interest. (See the RDF Semantic Graph Developer’s Guide for details about the Oracle SQL SEM_MATCH table function.) The other operations can further expand the graph. The Get Class Representative Summary returns summary information about a class representative. The Get Instance Summary returns summary information about a specific instance. Root Classes displays all the root classes in the graph Expand Class, Expand Object, and Expand Property operations can be performed on the graphs returned in the preceding operations to selectively expand a class, node, or property, respectively.
Menu Overview The menu options fall into the following categories:
Oracle Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2 12
Use the Root Nodes menu option at any time to view the primary nodes of a graph. Root classes are automatically displayed once the connection to Oracle Database is established and the model and rulebase information is loaded. This view displays all the root nodes in the class. If there are no root classes in the model, then an empty screen is displayed. In this case, you can start by displaying a subset of the data set using Get Subset.
View schema elements using the operations Get Demographics, Get Schema Demographics, Get View Metadata, and Toggle Overlay for information about the metadata for the selected view.
Explore and expand a graph using node and property level operations: o Expand Class displays all first level subclasses of the selected class. o Expand Object displays all nodes that are one hop away from the selected node. o Expand Property displays the expanded property list for the selected edges. o Get Class Representative Summary displays a summary of the instances for a class. o Get Instance Summary displays a summary for a particular instance.
Perform a query to visualize a subset of the graph. Queries can include filter conditions, such as the SQL WHERE clause, ROWNUM clause, etc. o Get Subset specifies a SPARQL-like Oracle SQL SEM_MATCH query and displays the sub-graph. o Get Subset Summary is similar to Get Subset but allows you to specify a focal point. o Facets allows you to browse the facets of a large data set efficiently. It returns all the individual sub-graphs matching the query pattern and allows you explore the resulting sub-graphs.
Search with keywords to build a Get Subset query. If you want to specify a value (RDF resource) for a node (subject or object) or a predicate in the query but don’t know its Uniform Resource Identifier (URI) you can search for it by specifying part of the resource name in the subject, predicate, or object. A list of up to forty matching names is displayed. You can select the URI of the resource and enter it in the triple pattern.
Literals can be hidden to present a more streamlined graph using the right-click menu.
Recalculate Label Counts is used to update the aggregate edge counts for any expanded edges.
Quick Tour: A FAMILY Social Network A sample data set for a Family Social Network (FAMILY) is used for this example. The following figures show the graphs that result from various operations.
The root classes are loaded when the support for Cytoscape connects to the database and loads the semantic model corresponding to the dataset. Figure 6 shows that #Resource is the only root class.
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Figure 6. Root class When the #Resource class is expanded, the graph has several subclasses (Person, Male, Female, Class, etc.)
Figure 7. The class hierarchy of the root node
Right click on the #Person node and get a particular Instance Summary, in this case, the pattern to
Oracle Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2 14 search for is the name Matt.
Figure 8. The Instance Summary of the node labeled as “Matt”
The sequence in Figure 9 shows the effect of the OVERLAY option when the Expand Property operation is performed on the edge for #type.
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Figure 9. OVERLAY option
Schema Operations Once a model is loaded and selected, schema operations can display the metadata for the current view of the model. You can simultaneously open multiple views of the same or different models.
Get Demographics menu command returns the demographics for the model, such as the number of distinct subjects, predicate, objects, and triples in the model.
Get Schema Demographics returns the information about the schema level statistics for the model, such as the total number of subclasses, and the maximum fan out of a node in the graph.
Get View Metadata displays information about the selected view, including the model, the rulebase used for displaying the entailed graph, the sample size selected, and whether the Overlay option is on.
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Figure 10. Get demographics operation Note that you must click OK in the window that displays the metadata information before you can proceed with other operations in Cytoscape.
Node and Property Operations Once a semantic model is loaded and its root classes are displayed in Cytoscape, you can explore the graph with node and property operations. Select a node or edge and use the context sensitive right-click menu as shown in Figure 11 and Figure 12, or the menu bar.
Get Class Representative Summary displays a summary of the instances for a class. The properties that the instances of a class could have are represented in the summary. Both incoming and outgoing property edges are displayed and a count is given for each edge indicating the number of instances having that property.
Get Instance Summary displays a summary for an instance of the class. The incoming and outgoing edges indicate the properties of the instance. A count is provided if there are multiple edges of the same type.
Expand Class displays all the immediate subclasses of a selected node.
Expand Node operation expands the subclasses of the selected node, and its properties and instances. It displays all of the triples that have the selected node as a subject or an object.
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Figure 11. Node context menu invoked from the right-click menu.
Expand Property displays the property list for an edge; it shows the individual property edges. Select the edge and using right-click menu as shown in Figure 12. When there are a large number of triples, pagination can be used to create and browse the multi-page list.
Expand with selective can be used to expand an edge using a selective query pattern or keyword. All the triples matching the keyword will be displayed.
Note: Expand Class and Expand Property operations can return a large number of triples. If the number of edges resulting from property expansion is too large to be displayed on the graph without clutter only the first K property edges are displayed. This restriction is set in the result returned by the database and/or the number of triples displayed by Cytoscape.
Figure 12. Property context menu invoked from the right-click menu Oracle Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2 18
Search for a Concept
To search for a concept in the RDF model, press the Search button in the left upper corner as shown in Figure 13. This will display a window dialog. Enter a concept to search as shown in Figure 14.
Figure 13. The button to perform a keyword-based search of triples
After a keyword has been entered and the query submitted, a list of triples is displayed. If you select a triple and press the Instance Summary button, the sub-graph containing this triple is displayed.
Figure 14. The list of triples that match with a keyword
To perform a keyword search, first create a full text index for the current selected model.
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Instance Summary To query an instance of a specific class, right-click over the node representing the class, and select the option Get Instance Summary as shown in Figure 15. Then specify a keyword or the URI for an instance of interest. This option can also be invoked from the menu bar after a node has been selected.
Figure 15. Get Instance Summary option invoked from the right-click menu
Visualizing a Subset of a Graph Once a semantic model is loaded and its root classes are displayed, you can explore the graph with the Node and Property operations previously described or by issuing a SPARQL query for a subset of nodes in the graph. As described in the next three sections, use the Get Subset menu item to specify a query pattern. Use Get Subset Summary to obtain a summary of a graph or a subgraph based on a focal point. Use Facets to perform efficient queries over large data sets. Get Subset The Get Subset option can be invoked from the right-click menu or the menu bar. The dialog in Figure 16 is displayed. You can enter a custom query and include up to ten triple patterns by clicking on the “+” button. Click Submit to enter the query. The results of the query are displayed as a graph.
For example, grandfathers can found with the following SPARQL query pattern:
{ ?s
This SPARQL query is entered in the Get Subset dialog as follows.
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Figure 16. Get subset window Query Options: Keyword searches can be performed to find URIs for the subject, predicate and object elements of a query by entering a keyword in the text field and clicking the search icon. A list of up to forty matches is displayed in a drop-down list. Subset queries can include SQL filter clauses, such as the WHERE and ROWNUM clauses. Subset queries can be named and saved for reuse. Selecting a stored query causes it to be loaded into the triple patterns where it can be edited and executed. Click Show Subgraphs to display a list of matching subgraphs as seen in Figure 19. Clicking Submit returns a graph of the grandfather subset in Figure 17:
Figure 17. Get Subset result Oracle Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2 21
Note: Get Subset operations can return a large number of triples. If the number of edges resulting from property expansion is too large to be displayed on the graph without clutter only the first K property edges are displayed. This restriction is set in the result returned by the database and/or the number of triples displayed by Cytoscape. Get Subset Summary Get Subset Summary is used to obtain a summary of the graph or sub-graph based on a focal point. For example, a wildcard query that has a “?s” focal point, returns the subset summary in Figure 18.
Figure 108. Get Subset Summary result
The subgraphs panel shows the query and the subgraphs resulting from the query. A list of subgraphs is located in the upper left of the window as seen in Error! Reference source not found.9. Select a subgraph from the list to highlight the subgraph on the right. Selecting a triple from the list on the lower left highlights the subgraphs that contain the selected triple.
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Figure 119. The subgraphs panel allows interaction with the subgraphs queried and the triples.
Facets Option Use the Facets button in the Subset Query window to browse the facets of a subset query more efficiently for a large data set. A pair of graphs showing facets of the subgraph is created, a “query- refinement” graph and an “original query pattern” graph. Figure 20 shows an example of both graphs.
The query-refinement graph in the box on the left displays a hierarchy of queries. There is one node for each query. The corresponding edge has the value of the variable for the child query. “Q1” is currently selected. It is the original query. The child nodes that branch from “Q1” are the finer-grained queries; they can also be examined. The query graph on the right shows the query structure for the selected query. Each node and edge is a variable in the query pattern. The number in parenthesis for each is the total number of distinct values for that variable in the data.
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Figure 20. The query refinement graph is on the left with the query pattern for the selected query “Q1” on the right.
Figure 21 shows the Apps -> Facets menu options that are available by right clicking on a node in the query refinement graph: Execute query will visualize the matching triples in a subgraphs panel as shown in the previous section. Show query-refinement-graph changes the query pattern to show facet values for the selected node in the query refinement graph. For example, selecting the node Q2 would display a graph with the node op1 replaced by the value Adrian. View SQL Query shows the SQL used to query the graph in Oracle Database.
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Figure 21. The facets menu option includes the execution of the current query and to show the facets result of a specific refinement node. Analyzing the Paths Between Nodes Common questions when an RDF model is analyzed include: Is there a path connecting two elements? What is the separation degree in this path? These questions can be answered with the Path finder option, located in the top level menu.
The Path finder dialog is shown in Figure 22. Analyze a path by entering a pattern in the text field and clicking the search button. The results of the search will be inserted in the boxes below the text fields.
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Figure 22. The Path finder dialog
Specifying the origin and target allows support for Cytoscape to calculate the distance from each node. All the paths having a distance less than or equal to the distance in the distance slider will be retrieved.
The subgraph panel in Figure 23 shows the results of the query from Figure 22. In this case, there are seven paths identified as sub-graphs. The user can select a subgraph from the list to highlight the associated triples in the table or select a triple from the table to highlight the associated subgraphs.
For example, selecting the triple [Tom -> type -> Person] highlights sub-graphs two and seven.
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Figure 23. Analyzing the Paths Between Nodes
Recalculating Label Counts Recalculate Label Counts is used to update the aggregate edge counts for any expanded edges. The edge counts are not updated automatically. If a node has multiple edges with the same predicate, the edge is compacted and is shown as an aggregate edge with an edge count. The edge count indicates the numbers of triples that are incoming and outgoing with the same predicate.
If you expand the graph through a series of operations, the aggregate edge count becomes incorrect and needs to be adjusted to account for the expanded edges. Recalculate Label Counts recalculates the aggregate edge count and updates the edge label.
For example, the aggregate count on the incoming #type property for Person in Figure 24 is incorrect, since there is already an explicit expanded edge #type. Figure 25 reflects the corrected edge count after Adjust Label Count is executed.
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Figure 124. Incorrect label count.
Figure 135. Corrected count after recalculating label counts.
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Color settings Color settings in Figure 26 enables filtering in or out the label or the predicates in the sub-graph, as well as changing the color of the edges and nodes. It is invoked using the Filter icon located in the right menu.
Figure 146. The Filter Predicates interface
The color assigned to each edge or predicate can be changed as shown in Figure 27. It shows the changed colors in the subgraph, according to the colors in Figure 26.
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Figure 27. Custom coloring of edges
Color settings for nodes
Color settings for the nodes can also be configured using the interface shown in Figure 28. The nodes are grouped according to the following types: URI’s, literals, blanks, query graph nodes, query- refinement graph nodes and a no-fill option for nodes.
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Figure 28. The node color interface
Data Set Sizes The table lists the size of a data set resulting from various operations.
Operation Type Result Size Default (Get Root Classes) Static Subset Get Demographics Static Summary 1 Get Class Demographics Static Summary 1 SEM_MATCH Dynamic Subset Summary [2*num_predicates] (with focal point) SEM_MATCH Dynamic Subset [0,num_triples]
Get Representative Summary Static Subset Summary [2*num_predicates] (for a class instance set)
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Operation Type Result Size Get Particular Instance Static Subset Summary [2*num_predicates] Summary Expand Class Dynamic Subset [0, num_triples]
Expand Object Dynamic Subset Summary [2*num_predicates]
Expand Property Dynamic Subset [0,num_triples]
Effect of OVERLAY Option on the Displayed Graph The following table describes how OVERLAY=YES option works. OVERLAY=NO will always display the resulting graph in a new view.
Operation Old New OVERLAY Annotated Annotated =YES Graph Graph Load Model N/A Singleton node New View (getRootClasses) Set SEM_MATCH Subset N/A Triple Set New View SEM_MATCH N/A Summary based New View Summary Triple Set Class Representative N/A Summary based New View Summary Triple Set Particular Instance N/A Summary based New View Summary Triple Set Expand Class AGold AGold U AGnew Old View Expand Object AGold AGold U AGnew Old View Expand Property AGold AGold U AGnew Old View
Adjusting The Edge Size, Shape And Background Colors The support for Cytoscape lets you configure the edge shape and color. The option, Color and Edge Configuration located in the menu bar displays a small configuration window to modify the background colors for the options, the edge shape and size, the node’s shape, and whether animations should be used. These configuration options are shown in Figure 29.
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Figure 29. General settings configuration window
If the option to use animation is set to true, then the nodes included in the expansions are added to the current graph without the use of animation. Figure 30 shows the result of applying color customization on edges and nodes on the current network or graph.
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Figure 30. The graph result of applying customization on nodes and edges
Construct Queries The menu option Construct query provides a dialog to create a query, as shown in Figure 31
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Figure 31. The construct query dialog
Shortcuts for the Most Used Features Icons in the menu provide shortcuts for the most used features. Figure 32 shows the menu with the shortcuts as described below from left to right:
The first icon expands the hierarchy of the selected nodes. It expands all the
Figure 32. The shortcuts to the most used features.
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Saving the Steps that Created the Current View
The sequence of steps performed by the user for the current visualization is recorded in the panel on the left as shown in Figure 33. The copy to clipboard button can save the sequence for future use.
Figure 33. The panel that displays the sequence of steps in the current visualization
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Oracle® Spatial and Graph RDF Semantic Graph Developer’s Guide 12c Release 1 – Graph Visualization Using Cytoscape 3.2 February 2016
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