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In Silico Biology 5, 0047 (2005); ©2005, Bioinformation Systems e.V.  

Ontology based standardization of Petri net modeling for signaling pathways

Takako Takai-Igarashi

Graduate School of Information Science and Technology, University of Tokyo, 7-3-1, Hongou, Bunkyou-ku, Tokyo 113-0033, Japan


Edited by E. Wingender; received July 24, 2005; revised and accepted September 24, 2005; published September 25, 2005


Taking account of the great availability of Petri nets in modeling and analyzing large complicated signaling networks, semantics of Petri nets is in need of systematization for the purpose of consistency and reusability of the models. This paper reports on standardization of units of Petri nets on the basis of an ontology that gives an intrinsic definition to the process of signaling in signaling pathways.

Keywords: Petri net, signaling pathway, ontology, knowledge representation