Update phase3 gene scaffolding to expand network

[abargnesi]

The phase3 gene scaffolding algorithm is inaccurate. The algorithm expands the g(A) transcribedTo r(A) translatedTo p(A) chain based on a BEL document using EntrezGene ids. The algorithm should infer this chain using the compilation unit's declared namespace.

For example if the compilation unit contains p(HGNC:A) then add

g(HGNC:A) transcribedTo r(HGNC:A)
r(HGNC:A) translatedTo p(HGNC:A)

If these statements already exist (even using equivalent terms) then skip. The BEL author may have already provided the scaffolding in which case the inference is redundant.

The benefits to this enhancement are:

• Expansion using the declared namespace
• Namespace decision left to the BEL author
• One less document to manage
• Faster algorithm