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OpenBEL / openbel-framework

An open platform for capturing, integrating, storing, and sharing biological knowledge in and across organizations.
http://openbel.org
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Expand rateLimitingStepOf relationships #50

Open nbargnesi opened 12 years ago

nbargnesi commented 12 years ago

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 commented 12 years ago

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 commented 12 years ago

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.