Part of a series beginning with:
With the last post, we have a dataset generated from Wordnet according to our data model, imported into a Vital Service Endpoint, which could be on our local machine or available remotely. For simplicity, we’ll assume it’s a local endpoint.
Cytoscape 3.X (the current version) allows creating “apps” (formerly known as “plugins”) that allow adding additional functionality to the Cytoscape desktop application.
The documentation for creating such apps can be found here: http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper
Cytoscape supports the OSGI standard ( http://en.wikipedia.org/wiki/OSGi ), which can be a little tricky. However, it provides a general way to include dependencies.
The source code for the Vital Service Cytoscape App is found on github here: https://github.com/vital-ai/vital-cytoscape
The two main implemented functions are: (1) searching the Wordnet data for a matching SynsetNode, and (2) given a particular Wordnet SynsetNode, performing a graph query to add all connected Edges and Nodes into the current graph.
For the first case, the “search” function is run in the SearchTab to produce a set of matching SynsetNodes. The snippet of code in SearchTab is:
ResultList rs = Application.get().search(selectquery);
For the second case, the “Expand Node” function is run when it’s selected by using the contextual menu on a Node (or set of Nodes). The snippet of code in ExpandNodeTask is:
ResultList rs_connections = Application.get().getConnections(uri_string);
Within the Application class, we connect to VitalService and perform the select query, returning the found objects:
ResultList rlist = Factory.getVitalService().selectQuery(sq);
Within the Application class, we connect to VitalService and “expand” a graph object, triggering getting all the connected Nodes and Edges into the local cache, which we can then display.
GraphObject graphObjectExpanded = Factory.getVitalService().getExpanded(VitalURI.withString(uri_str), getWordnetSegment())
The Vital AI Cytoscape App adds some tabs and contexual menus to the Cytoscape User Interface.
Here’s the Search Tab displaying search results:
and here is the contextual menu associated with a SynsetNode, used to trigger “expanding” the Node:
Put it all together, and we can explore graph data stored in a Vital AI Endpoint using our new Cytoscape App!
Next we’ll use some Graph Analytics to help visualize our data.