Reconstruction of protein-protein interaction pathways by mining subject-verb-objects intermediates

Authors:
Maurice H. T. Ling;Christophe Lefevre;Kevin R. Nicholas;Feng Lin
Affiliations:
BioInformatics Research Centre, Nanyang Technological University, Singapore and CRC for Innovative Dairy Products, Department of Zoology, The University of Melbourne, Australia;Victorian Bioinformatics Consortium, Monash University, Australia;CRC for Innovative Dairy Products, Department of Zoology, The University of Melbourne, Australia;BioInformatics Research Centre, Nanyang Technological University, Singapore
Venue:
PRIB'07 Proceedings of the 2nd IAPR international conference on Pattern recognition in bioinformatics
Year:
2007

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Abstract

The exponential increase in publication rate of new articles is limiting access of researchers to relevant literature. This has prompted the use of text mining tools to extract key biological information. Previous studies have reported extensive modification of existing generic text processors to process biological text. However, this requirement for modification had not been examined. In this study, we have constructed Muscorian, using MontyLingua, a generic text processor. It uses a two-layered generalization-specialization paradigm previously proposed where text was generically processed to a suitable intermediate format before domain-specific data extraction techniques are applied at the specialization layer. Evaluation using a corpus and experts indicated 86-90% precision and approximately 30% recall in extracting protein-protein interactions, which was comparable to previous studies using either specialized biological text processing tools or modified existing tools. Our study had also demonstrated the flexibility of the two-layered generalization-specialization paradigm by using the same generalization layer for two specialized information extraction tasks.