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Extracting kinetic information from literature with KineticRE

Alão Freitas, Ana ; Costa, Hugo ; Rocha, Miguel ; Rocha, Isabel

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
To better understand the dynamic behavior of metabolic networks in a wide variety of conditions, the field of Systems Biology has increased its interest in the use of kinetic models. The different databases, available these days, do not contain enough data regarding this topic. Given that a significant part of the relevant information for the development of such models is still wide spread in the literature, it becomes essential to develop specific and powerful text mining tools to collect these data. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites. The approach proposed integrates the development of a novel plug-in over the text mining framework @Note2. In the end, the pipeline developed was validated with a case study on Kluyveromyces lactis, spanning the analysis and results of 20 full text documents.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Alão Freitas, Ana ; Costa, Hugo ; Rocha, Miguel ; Rocha, Isabel  (2015)  Extracting kinetic information from literature with KineticRE. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 12(4): Special Issue: Selected extended papers of the 9th International Conference on Practical Applications of Computational Biology and Bioinformatics, Salamanca, Spain, 2015. Guest editors: Florentino Fdez-Riverola, Juan F. De Paz, Ross Overbeek and Miguel Rocha

Online-Journal: http://journal.imbio.de/
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2015/5421



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