I'm trying to build a webpage on which embed a visualization window for my local graph database. The graph database I'm using is Neo4j and for visualization I'm trying to use Cytoscape. Until now, I embedded a test graph in a webpage thanks to Cytoscape.js by putting some nodes and relationships directly in the JavaScript code. The only thing I still have problem with is the connection between Cytoscape and my local Neo4j Database. Which would be the best way to do this?
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Typically, I answer Cytoscape desktop (not Cytoscape.js) questions, but I have built a web site (see https://spoke.rbvi.ucsf.edu) that does exactly what you are proposing. For a number of reasons, we implemented it with an intermediate REST interface so that we don't have to expose our Neo4J database. The REST interface does all of the queries and spits out cytoscape.js JSON formatted networks...