In my StackOverflow post, Creating a metabolic pathway in Neo4j I describe how I created and linked two metabolic pathways (glycolysis and the TCA cycle) in Neo4j.
Please refer to that post, as it is very complete.
Notably, in my “follow-on” answer (there), I describe an issue that initially vexed me – and my solution:
... An issue that arose during the creation of my `TCA pathway` graph was that the one of the nodes (the enzyme, `aconitase`) was used twice, so during the graph creation `MERGE` merged the common node `aconitase` as a single entity, resulting in this layout,
... not this one, as desired,
My solution to that issue was to create the `TCA graph` using node properties, to temporarily differentially-tag the affected source and target nodes (later removing those tags, after the graph was properly created). ...
[ … SNIP! … ]
Here is that final graph, in the Neo4j Browser:
[Click the image for a full-size version.]