OrthoDB - add option to use protein ID field

[julie-sullivan]

configuration file that determines which fields are set in the OrthoDB converter

taxonId.geneid = which gene field to set
if identifier is not set, primaryIdentifier will be used

if ID resolver is used, will use to look up non-Ensembl ID and put in the primary
identifier field

worm - Secondary Id
83333.geneid=secondaryIdentifier

[mlyne]

Currently, the converter grabs field 4 (Gene_ID) but this is not useful for bacteria. We need Field 3 (Protein_ID).

ODB6_Level ODB6_OG_ID Protein_ID Gene_ID ... OtherFields
Firmicutes-Bacilli EOG600VNV BA_2196 30262211 ... OtherFields

See example test file:

/intermine/bio/orthodb/test/resources/OrthoDB_test

SynBioMine needs to have Orthologues loaded soon as it is now on the critical path as it may hold up the work of the part III student.