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

conference contribution
posted on 2007-01-01, 00:00 authored by M H T Ling, C Lefevre, Kevin Nicholas, F Lin
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 genetically 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 proteinprotein 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. © Springer-Verlag Berlin Heidelberg 2007.

History

Volume

4774 LNBI

Pagination

286 - 299

ISSN

0302-9743

eISSN

1611-3349

ISBN-13

9783540752851

Title of proceedings

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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