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we were solving similar problem. We incorporated the "Approved Commodities" field into the Supplier Profile Questionnaire (SPQ) and mark this field as an internal field (not visible for suppliers). Then we uploaded existing suppliers to Ariba by a mass upload and subsequently also exported SPQs for them from Ariba. We received the SPQs in a form of CSV so we were able to fill in the "Approved Commodities" field with values from old system and import SPQs back to the system. From that moment we manage approved commodities only in Ariba.
You can find the Export/Import of SPQs in Ariba as "Supplier Profile Import/Export" in menu Administration.