you check the built in services in WMEDI package, you should be able to list all external Id types and their associated qualifiers. you make use of this service.
Since you are receiving EDI inbound into webMethods then,you can extract/check those EDI duns values from the ISA level
ISA05(Qualifier),ISA06(Duns#) using envelopeProcess service and put a conditionlogic in your map.
If not please elaborate more info on your requirement…to do’s etc…