This paper presents a nonmonotonic ILP approach for the automatic revision of metabolic networks through the logical analysis of experimental data. The method extends previous work in two respects: by suggesting revisions that involve both the addition and removal of in- formation; and by suggesting revisions that involve combinations of gene functions, enzyme inhibitions, and metabolic reactions. Our proposal is based on a new declarative model of metabolism expressed in a non- monotonic logic programming formalism. With respect to this model, a mixture of abductive and inductive inference is used to compute a set of minimal revisions needed to make a given network consistent with some observed data. In this way, we describe how a reasoning system called XHAIL was able to correctly revise a state-of-the-art metabolic pathway in the light of real-world experimental data acquired by an autonomous laboratory platform called the Robot Scientist.