mgi: changes to Transgenes
mgi: changes to Transgenes

* when a transgene is unlocated, don't create a separate sequence alteration node.  Make the transgene itself the sequence alteration, and make it sameAs/equivalentTo the marker.  This is done with a bit of a hack to see if it includes the pattern "Tg(" which all transgenic alleles contain.
* add the value of the allele key as a comment
* remove Not Applicable and Not Specified from derives_from [strain] pattern
* move testing for nobnodes into the makeInternalIdentifier method
* change relationship derives_from --> sequence_derives_from between a Tg construct and the gene it gets sequence from
* update a few SO mappings that were out of date (chromosomal_inversion, robersonian fusion)

TomConlin/dipper,monarch-initiative/dipper,monarch-initiative/dipper,TomConlin/dipper,monarch-initiative/dipper