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Event based text mining for integrated network construction

Yvan Saeys UGent, Sofie Van Landeghem and Yves Van de Peer UGent (2010) JMLR Workshop and Conference Proceedings. 8. p.112-121
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
Please use this url to cite or link to this publication:
author
organization
year
type
conference
publication status
published
subject
keyword
integrated networks, event extraction, Text mining
in
JMLR Workshop and Conference Proceedings
editor
Sašo Džeroski, Pierre Geurts and Juho Rousu
volume
8
issue title
Machine learning in systems biology : proceedings of the third international workshop on machine learning in systems biology
pages
112 - 121
publisher
Microtome Publishing
place of publication
Brookline, MA, USA
conference name
3rd International workshop on Machine Learning in Systems Biology (MLSB 2009)
conference location
Ljubljana, Slovenia
conference start
2009-09-05
conference end
2009-09-06
ISSN
1938-7288
language
English
UGent publication?
yes
classification
C1
copyright statement
I have retained and own the full copyright for this publication
id
2093782
handle
http://hdl.handle.net/1854/LU-2093782
date created
2012-04-24 18:47:17
date last changed
2017-01-02 09:53:05
@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},
}

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.