Finding kinetic parameters using text mining

OMICS. 2004 Summer;8(2):131-52. doi: 10.1089/1536231041388366.


The mathematical modeling and description of complex biological processes has become more and more important over the last years. Systems biology aims at the computational simulation of complex systems, up to whole cell simulations. An essential part focuses on solving a large number of parameterized differential equations. However, measuring those parameters is an expensive task, and finding them in the literature is very laborious. We developed a text mining system that supports researchers in their search for experimentally obtained parameters for kinetic models. Our system classifies full text documents regarding the question whether or not they contain appropriate data using a support vector machine. We evaluated our approach on a manually tagged corpus of 800 documents and found that it outperforms keyword searches in abstracts by a factor of five in terms of precision.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology*
  • Databases as Topic
  • Humans
  • Information Management
  • Information Storage and Retrieval / methods*
  • Kinetics
  • Models, Theoretical*
  • Periodicals as Topic