Automatic extraction of kinetic information from biochemical literatures

Authors:
Jyh-Jong Tsay;Bo-Liang Wu;Chang-Ching Hsieh
Affiliations:
Dept. of Computer Science & Information Engineering, National Chung-Cheng University, Chia-Yi, Taiwan;Dept. of Computer Science & Information Engineering, National Chung-Cheng University, Chia-Yi, Taiwan;Dept. of Computer Science & Information Engineering, National Chung-Cheng University, Chia-Yi, Taiwan
Venue:
FSKD'09 Proceedings of the 6th international conference on Fuzzy systems and knowledge discovery - Volume 5
Year:
2009

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Abstract

Software for computational analysis and simulation of biochemical systems has become one of the major computational tools in systems biology in recent years. Most of them use parameterized differential equations to model and describe biochemical systems. Although biochemical principles, such as enzyme mechanics, have been developed to derive kinetic rate equations, measuring and providing parameters in the equations are expensive and laborious. Observe that many kinetic parameters have been experimentally measured in previous research, and recorded in published literatures. Instead of measuring kinetic parameters from experiments, one of the alternatives is to find parameters from literatures. However, the amount of such literatures is huge, and reading them is very time-consuming. About the previous research of kinetic parameters are focused on literature including kinetic parameters or not. In this paper, we present a software tool (KIND) for automatic extraction of kinetic parameters from full-length literatures. In order to help biologist easy to retrieve kinetic parameters information, KIND can automatic generate table format to present kinetic parameters information from literatures. We aim at developing a tool that can be used to compile a database of kinetic parameters from literatures to aid the modeling of biological processes.