Manually switched all Term Accession Number and Term Source REF from all isa entries from study and assays as these seem to remain being switched. Also corrected these in assay and study is files. This was a bug in the arccommander where the respective flags were changed and arguments passed via these were inserted in the opposing field, respectively for studies and assays. Also added manually the ontology source references of the ontologies from the study and assay part as these currently (v0.5.0 used fort this ARC) can not be passed via arccommander.