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A nonmonotonic logical approach for modelling and revising metabolic networks

Oliver Ray, Ken Whelan, Ross King, A nonmonotonic logical approach for modelling and revising metabolic networks. 3rd International Conference on Complex, Intelligent and Software Intensive Systems (from 2nd International Workshop on Intelligent Informatics in Biology and Medicine), pp. 825–829. March 2009. PDF, 195 Kbytes.

Abstract

This paper describes a new logic-based approach for representing and reasoning about metabolic networks. First it shows how biological pathways can be elegantly represented in a logic programming formalism able to model full chemical reactions with substrates and products in different cell compartments, and which are catalysed by iso-enzymes or enzyme-complexes that are subject to inhibitory feedbacks. Then it shows how a nonmonotonic reasoning system called XHAIL can be used as a practical method for learning and revising such metabolic networks from observational data. Preliminary results are described in which the approach is validated on a state-of-the-art model of Aromatic Amino Acid biosynthesis.

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