Oracle Spatial and Graph – technical tips, best practices, and news from the product team

Powerful and Effective Graph Visualization with Cytoscape and Oracle's Property Graph Database (2)

Alan Wu

In this installment of the Cytoscape visualization for Oracle's Property Graph Database series, I am going to talk about key steps required to set up Cytoscape visualization for Oracle's Property Graph Database. These steps are the same for Oracle Spatial and Graph (OSG), and Oracle Big Data Spatial and Graph (BDSG).

Assume you are using Linux or Mac OS. The major steps are as follows.

0) Make sure you have Oracle JDK 8. 

1) Download & install Cytoscape (3.2.1 or above). Assume you install Cytoscape under 
2) Start Cytoscape to initialize. Make sure the following directory is created

   Once the above directory is created, quit Cytoscape.

3) cd /Applications/Cytoscape_v3.6.1 

4) Unzip the Cytoscape plugin for OSG (or BDSG) in the above directory. 
    A new sub directory will be created. The directory name is oracle_property_graph_cytoscape/
    if you are using Cytoscape plugin for Oracle Database.

5) Copy propertyGraphSupport*.jar from the jar/ in the above sub directory into 

6) Copy propertyGraph.properties from the jar/ in the above sub directory into
   To customize this configuration, follow the usage guide (a PDF file you can find in the Cytoscape plugin zip file).

7) kick off Cytoscape by running the following under /Applications/Cytoscape_v3.6.1 

    sh ./startCytoscape.sh 

   NOTE: it is important to use startCytoscape.sh to start the visualization. Do not use the original cytoscape.sh because you will not see any property graph related functions (highlighted below).





[1] http://www.oracle.com/technetwork/database/options/spatialandgraph/downloads/index-156999.html

[2] Oracle Big Data Spatial and Graph Downloads



Join the discussion

Comments ( 2 )
  • Narayanan Thursday, September 5, 2019
    Is it possible to view a graph that is created in a standalone PGX server in cytoscape directly without having to connect to a Oracle NoSQL or Oracle Database? (I have been able to complete all the configuration steps mentioned above and see the property graph related functions in cytoscape)?
  • Jim Steiner Wednesday, January 8, 2020
    Apologies for the delay in responding to your inquiry. (There was an issue with the notification workflow in the Blog system).
    Today, you should be able to export the graph from the PGX server in GraphML format, which Cytoscape supports and will enable you to visualize the graph and use the features in Cytoscape. We are looking at the possibility of having a
    Cytoscape plug-in in the future that can directly work with a PGX instance to execute algorithms against a graph and visualize the results.
Please enter your name.Please provide a valid email address.Please enter a comment.CAPTCHA challenge response provided was incorrect. Please try again.