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Different databases of metabolic pathways assign pathways different keys. For this reason, it is difficult to automatically compare pathways across databases. We introduce an algorithm called the Universal Pathway Key algorithm or UPK that assigns essentially unique keys to metabolic pathways. We show that the UPK algorithm assigns unique keys to the pathways in the MetaCyc database and can also be used to detect duplicate pathways. The UPK algorithm is a simple generalization of the UCK algorithm introduced in  that assigns essentially unique keys to chemical compounds.