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This is free, open source, standalone tool written in Java, to create simple directed graphs using the Reactome Graph Database and Uniprot.
From the definition, a directed Graph G = (V, A) is formed by a set of Vertices V and a set of Arcs A, where arcs are directed connections between the vertices. In our case, the Vertices are Reviewed Human Proteins and the Arcs are Protein Interactions.
The protein interactions can be of several types relating to their roles in the reactions in Reactome. We say two proteins P1 and P2 are interacting if both belong to the same reaction R and have different roles. For example, P1 is Reactant (input) and P2 is Product (output); or P1 is Catalyst and P2 is Product (output). Note that these interactions are represented by directional edges (arcs), because the roles are fixed for P1 and P2. For a full list of the possible edge types in the graph check the configuration.
Some protein interactions, like being complex neighbours, are bidirectional, in which case two arcs are used to represent this interaction, one from P1 to P2 and one from P2 to P1.
There is a version implemented in R and another in Java.