consolidate increases and directlyIncreases edges during KAM compilation

[ncatlett]

In the BEL Framework 2.0.0, similar edge types connecting the same nodes are not consolidated. Ideally, the compiler should consolidate to the edge type that provides the most information.

E.g., consolidate to a single KAM edge, preserving the underlying statements:

directlyIncreases, increases, positivecorrelation, and association

directlyDecreases, decreases, negativeCorrelation, and association

[tedslater]

Just for the sake of argument:

1) If the BEL edge distinctions are useful, why not preserve the semantics in the KAM?

2) If the BEL edge distinctions are not useful, why preserve them in BEL?

[ncatlett]

1) One of the differences between edge types is the amount of information provided about the relationship from the reference and captured by the curator. For example, for the relationship A directlyIncreases B, the less specific relationships (A increases B, A positivelyCorrelates B, and A association B) also hold true. Without consolidation, 4 edges are possible to connect source A to target B; this makes pathfinding and other network traversals more complex than necessary.

The statements supporting each edge should be maintained, and ideally consolidation of edges would be optional (the default).

2) It is important to maintain the edge types in BEL to capture the available information about a given relationship from a single source. E.g., to distinguish between direct interactions and interactions where the source and target are not known to physically interact. Also to distinguish causal relationships from correlative.