Q:

How can I relate an edge/relationship to a node which contains information about that edge?

I have to store biological interactions in a Neo4j database. For example, consider a scenario where I have two types of nodes, Protein & Experiment and a relationship INTERACTS_WITH. The relationship exists as (Protein)-[INTERACTS_WITH]-(Protein). Now, the INTERACTS_WITH also relates to Experiment because this biological interaction was observed in that experiment.
I need to relate the INTERACTS_WITH relationship to the Experiments.
One way to achieve this can be to store the ID of all such Experiments in an array type property of the INTERACTS_WITH relationship. But that will be just like storing the Primary Key of an entity as Foreign Key of another entity in the relational database, which I want to avoid.
Another way can be to create an Interaction node for each pair of interacting genes and then relate it to the two Proteins and the Experiments. But an interaction is possible between two Protein nodes only, so I will have to programmatically put a constraint on the number of Protein nodes that relate to an Interaction node. This approach is also not good because INTERACTS_WITH is actually a relationship and perhaps it will be not a good idea to model it as a node.
Is there a better, graphical way to do this? If not, which of the above two approaches will be better?

A:

Another way can be to create an Interaction node for each pair of
  interacting genes and then relate it to the two Proteins and the
  Experiments.

I believe that it is a very good approach to solve your problem. 

But an interaction is possible between two Protein nodes only, so I
  will have to programmatically put a constraint on the number of
  Protein nodes that relate to an Interaction node.

There is nothing to do. Programmers do it all the time! For example: What guarantees do you have about how many INTERACTS_WITH relationships exists between a pair of  Protein nodes? Probably you take care about it at creation time.

This approach is also not good because INTERACTS_WITH is actually a
  relationship and perhaps it will be not a good idea to model it as a
  node.

Think about it: if your INTERACTS_WITH relationship needs to be related with more than two nodes maybe you are modeling a node as a relationship, right?
Tip: take a look in the section Graph modeling – best practices and
pitfalls of the book Learning Neo4j (by Rik Van Bruggen) and in the section Common Modeling Pitfalls of the book Graph Databases (by Ian Robinson, Jim Webber & Emil Eifrem). This can be enlightening. You can download the two books in the Neo4j site here.

