Is there some online documentation on recommended patterns to use instead of the reference node? I know that I, for one, used the reference node for almost all data structures, very much like using '/' in unix. Without the reference node, I assume that all starting points need to be specified by node id, which should be obtained from an external source. I expect in most cases the external source will actually be the included lucene index, unless the app decided to add some other persistence feature. In this case perhaps the 'recommended pattern' would be a description of using lucene for start nodes. I believe this is already the case in most cypher examples, but perhaps not for embedded java usage.