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    Metabolic pathway mining

    Czarnecki, Jan and Shepherd, Adrian J. (2016) Metabolic pathway mining. In: Keith, J.M. (ed.) Bioinformatics Volume II: Structure, Function, and Applications. Methods in Molecular Biology 1526. New York, U.S.: Humana Press, pp. 139-158. ISBN 9781493966110.

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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.


    Item Type: Book Section
    Additional Information: Series ISSN: 1064-3745
    Keyword(s) / Subject(s): Metabolic pathway, Metabolic interaction extraction, Text-mining, Natural language processing, Named entity recognition, Information extraction
    School: School of Science > Biological Sciences
    Research Centres and Institutes: Data Analytics, Birkbeck Institute for
    Depositing User: Administrator
    Date Deposited: 07 Mar 2017 16:59
    Last Modified: 28 May 2020 13:32


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