Missing orthologous relationships

[ncatlett]

It appears that orthologous relationships are only added to nodes present in the network at the start of Phase III. geneAbundances added to the network via "gene scaffolding" are not getting connected via orthologous edges. Protein family nodes added as orthologs are not getting further orthologous edges (i.e., if human family is present in the network, mouse and rat orthologous nodes will be added, but not connected to each other by an orthologous edge.)

[abargnesi]

This is an issue with pruning the orthology documents down to knowledge that overlaps the compilation unit. The pruning algorithm relies on the orthology entity UUIDs which have not yet been computed.