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Event based text mining for integrated network construction

Yvan Saeys (UGent) , Sofie Van Landeghem (UGent) and Yves Van de Peer (UGent)
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Abstract
The scientific literature is a rich and challenging data source for research in systems biology, providing numerous interactions between biological entities. Text mining techniques have been increasingly useful to extract such information from the literature in an automatic way, but up to now the main focus of text mining in the systems biology field has been restricted mostly to the discovery of protein-protein interactions. Here, we take this approach one step further, and use machine learning techniques combined with text mining to extract a much wider variety of interactions between biological entities. Each particular interaction type gives rise to a separate network, represented as a graph, all of which can be subsequently combined to yield a so-called integrated network representation. This provides a much broader view on the biological system as a whole, which can then be used in further investigations to analyse specific properties of the network
Keywords
integrated networks, event extraction, Text mining

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Chicago
Saeys, Yvan, Sofie Van Landeghem, and Yves Van de Peer. 2010. “Event Based Text Mining for Integrated Network Construction.” In JMLR Workshop and Conference Proceedings, ed. Sašo Džeroski, Pierre Geurts, and Juho Rousu, 8:112–121. Brookline, MA, USA: Microtome Publishing.
APA
Saeys, Yvan, Van Landeghem, S., & Van de Peer, Y. (2010). Event based text mining for integrated network construction. In S. Džeroski, P. Geurts, & J. Rousu (Eds.), JMLR Workshop and Conference Proceedings (Vol. 8, pp. 112–121). Presented at the 3rd International workshop on Machine Learning in Systems Biology (MLSB 2009), Brookline, MA, USA: Microtome Publishing.
Vancouver
1.
Saeys Y, Van Landeghem S, Van de Peer Y. Event based text mining for integrated network construction. In: Džeroski S, Geurts P, Rousu J, editors. JMLR Workshop and Conference Proceedings. Brookline, MA, USA: Microtome Publishing; 2010. p. 112–21.
MLA
Saeys, Yvan, Sofie Van Landeghem, and Yves Van de Peer. “Event Based Text Mining for Integrated Network Construction.” JMLR Workshop and Conference Proceedings. Ed. Sašo Džeroski, Pierre Geurts, & Juho Rousu. Vol. 8. Brookline, MA, USA: Microtome Publishing, 2010. 112–121. Print.
@inproceedings{2093782,
  abstract     = {The scientific literature is a rich and challenging data source for research in systems biology, providing numerous interactions between biological entities. Text mining techniques have been increasingly useful to extract such information from the literature in an automatic way, but up to now the main focus of text mining in the systems biology field has been restricted mostly to the discovery of protein-protein interactions. Here, we take this approach one step further, and use machine learning techniques combined with text mining to extract a much wider variety of interactions between biological entities. Each particular interaction type gives rise to a separate network, represented as a graph, all of which can be subsequently combined to yield a so-called integrated network representation. This provides a much broader view on the biological system as a whole, which can then be used in further investigations to analyse specific properties of the network},
  author       = {Saeys, Yvan and Van Landeghem, Sofie and Van de Peer, Yves},
  booktitle    = {JMLR Workshop and Conference Proceedings},
  editor       = {D\v{z}eroski, Sa\v{s}o and Geurts, Pierre and Rousu, Juho},
  issn         = {1938-7288},
  keyword      = {integrated networks,event extraction,Text mining},
  language     = {eng},
  location     = {Ljubljana, Slovenia},
  pages        = {112--121},
  publisher    = {Microtome Publishing},
  title        = {Event based text mining for integrated network construction},
  volume       = {8},
  year         = {2010},
}