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,

image_1

... not this one, as desired,

image_2

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:

neo4j-glycolysis-tca.png

[Click the image for a full-size version.]