Exploiting knowledge ontology and software agents for PPI network analysis

Authors:
Wen-Shyong Tzou;Wei-Po Lee;Bingchiang Jeng
Affiliations:
Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan;Department of Information Management, National Sun Yat-sen University, Kaohsiung, Taiwan;Department of Information Management, National Sun Yat-sen University, Kaohsiung, Taiwan
Venue:
Expert Systems with Applications: An International Journal
Year:
2009

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Abstract

One major goal of functional genomics has been to identify and analyze molecular interactions in a cellular context to better understand the underlying design principles and mechanisms. To investigate into a PPI network from both topological and functional points of view, this work proposes a methodology that exploits ontology-based biological knowledge for network analysis. To speed up the procedure, an agent-based framework is also presented for supporting distributed computing. The preliminary results show that through the knowledge obtained from gene ontology, our work in analyzing building blocks of PPI networks can give a higher resolution than that of previous ones. Also our agent-based framework can successfully speed up the task of network analysis in an adaptive manner.