Remove accidentally re-added new() and ontology() methods.
Remove accidentally re-added new() and ontology() methods.

Make fetch_by_name() take an optional second argument (ontology name).

Make fetch_by_name() also look at synonyms.

muffato/ensembl,mjg17/ensembl,mjg17/ensembl,james-monkeyshines/ensembl,Ensembl/ensembl,Ensembl/ensembl,at7/ensembl,Ensembl/ensembl,muffato/ensembl,danstaines/ensembl,mjg17/ensembl,at7/ensembl,at7/ensembl,muffato/ensembl,danstaines/ensembl,at7/ensembl,willmclaren/ensembl,willmclaren/ensembl,james-monkeyshines/ensembl,danstaines/ensembl,james-monkeyshines/ensembl,mjg17/ensembl,muffato/ensembl,james-monkeyshines/ensembl,Ensembl/ensembl