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Bioinformatics 2005 21(Suppl 1):i319-i327; doi:10.1093/bioinformatics/bti1011
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Beyond the clause: extraction of phosphorylation information from medline abstracts

M. Narayanaswamy 1, K. E. Ravikumar 1 and K. Vijay-Shanker 2,*

1AU-KBC Research Centre, Anna University Chennai, India
2Department of Computer and Information Sciences, University of Delaware Newark, DE, USA

*To whom correspondence should be addressed.

Motivation: Phosphorylation is an important biochemical reaction that plays a critical role in signal transduction pathways and cell-cycle processes. A text mining system to extract the phosphorylation relation from the literature is reported. The focus of this paper is on the new methods developed and implemented to connect and merge pieces of information about phosphorylation mentioned in different sentences in the text. The effectiveness and accuracy of the system as a whole as well as that of the methods for extraction beyond a clause/sentence is evaluated using an independently annotated dataset, the Phospho.ELM database. The new methods developed to merge pieces of information from different sentences are shown to be effective in significantly raising the recall without much difference in precision.

Contact: vijay{at}cis.udel.edu

Received on January 15, 2005; accepted on March 27, 2005

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