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This is free, open source, standalone tool 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. First, two proteins P1 and P2 interact if both are members of the same complex or set in Reactom. Second, they interact if both belong to the same reaction and perform different roles in the reaction. The possible roles for a protein in a reaction are: input (reactant), output (product), catalyst and regulator. 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.