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Briefings in Bioinformatics 2005 6(3):263-276; doi:10.1093/bib/6.3.263
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© Henry Stewart Publications

Extraction of biological interaction networks from scientific literature

Andre Skusa
PhD student at the NRW International Graduate School in Bioinformatics and Genome Research, Bielefeld University, Germany. His research focus is in reconstruction and analysis of biological interaction networks.

Alexander Rüegg
Research associate at the Bioinformatics and Medical Informatics Department of the Bielefeld University, Germany. His main research topics are text mining and data integration applied to protein-protein interaction networks.

Jacob Köhler
Bioinformatics Principal Investigator at Rothamsted Research, UK. His research interests include data integration, text mining as well as modelling and simulation of biological systems.


Andre Skusa, NRW Graduate School in Bioinformatics and Genome Research, Bielefeld University, Postfach 10 01 31, D-33501 Bielefeld, Germany Tel: +49 521 106 3955 E-mail: askusa{at}cebitec.uni-bielefeld.de

Biology can be regarded as a science of networks: interactions between various biological entities (eg genes, proteins, metabolites) on different levels (eg gene regulation, cell signalling) can be represented as graphs and, thus, analysis of such networks might shed new light on the function of biological systems. Such biological networks can be obtained from different sources. The extraction of networks from text is an important technique that requires the integration of several different computational disciplines. This paper summarises the most important steps in network extraction and reviews common approaches and solutions for the extraction of biological networks from scientific literature.

Keywords: network extraction, interaction networks, relation mining


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R. Chowdhary, J. Zhang, and J. S. Liu
Bayesian inference of protein-protein interactions from biological literature
Bioinformatics, June 15, 2009; 25(12): 1536 - 1542.
[Abstract] [Full Text] [PDF]


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