Expand rateLimitingStepOf relationships

[nbargnesi]

The RATE_LIMITING_STEP_OF relationship is defined as indicating for some A and B:

A rateLimitingStepOf B

implies:

A subProcessOf B
A increases B

Compiler expansion has typically treated relationships like rateLimitingStepOf as expanded to the implied relationships.

[ncatlett]

It may be preferable to leave it unexpanded, since expansion would result in two edges connecting the nodes, potentially making the network more difficult to interpret

[nbargnesi]

Agreed. We would make the default expansion behaviour consistent with the current compiler and provide whatever other capabilities as optional compiler flags.

Here are the options we've identified:

1. No expansion.

   Two nodes, A and B, connected by the edge rateLimitingStepOf. The statement
   supporting the edge is the statement from the BEL knowledge (e.g., A rateLimitingStepOf B).

2. Expansion.

   Two nodes, A and B, connected by two edges subProcessOf and increases. The
   statement supporting the subProcessOf edge is the statement A subProcessOf B.
   The statement supporting the increases edge is the statement A increases B. Both
   statements are injected by the compiler.

3. Expansion with preservation.

   Two nodes, A and B, connected by three edges (1) rateLimitingStepOf, (2) subProcessOf,
   and (3) increases. The statement support, respective of each edge, would be
   (1) A rateLimitingStepOf B, (2) A subProcessOf B and A rateLimitingStepOf B, and
   (3) A increases B and A rateLimitingStepOf B.