Be warned that Cytoscape is a different code base than Cytoscape.js. I have not used Cytoscape which uses Java. Cytoscape.js obviously uses JavaScript and needs a running server to present web pages.
The most complete example of using Cytoscape.js that I posted is found in this reply, click Details - Click triangle to expand. to see the code. Note that that example uses a Node.js server but IIRC I was also able to swap that out for an SWI-Prolog HTTP server thus obviating the need for node.js. The nice thing about that example is that it uses JSON data files which are easily created from SWI-Prolog dictionaries using IIRC json_write_dict/N. See
Json_dict/2 - Helpful for learning how to use JSON with SWI-Prolog dict for caveats. 