Volume 1526 of the series Methods in Molecular Biology pp 139-158


Metabolic Pathway Mining

  • Jan M. CzarneckiAffiliated withSchool of Biosciences, Birkbeck, University of London
  • , Adrian J. ShepherdAffiliated withDepartment of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London Email author 

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Understanding metabolic pathways is one of the most important fields in bioscience in the post-genomic era, but curating metabolic pathways requires considerable man-power. As such there is a lack of reliable, experimentally verified metabolic pathways in databases and databases are forced to predict all but the most immediately useful pathways.

Text-mining has the potential to solve this problem, but while sophisticated text-mining methods have been developed to assist the curation of many types of biomedical networks, such as protein–protein interaction networks, the mining of metabolic pathways from the literature has been largely neglected by the text-mining community. In this chapter we describe a pipeline for the extraction of metabolic pathways built on freely available open-source components and a heuristic metabolic reaction extraction algorithm.

Key words

Metabolic pathway Metabolic interaction extraction Text-mining Natural language processing Named entity recognition Information extraction