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Bioinformatics Advance Access published online on January 12, 2006
Bioinformatics, doi:10.1093/bioinformatics/btk044
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received October 20, 2005
Revised December 9, 2005
Accepted January 5, 2006

Article

LSAT: learning about alternative transcripts in MEDLINE

Parantu K. Shah 1 * and Peer Bork 1

1 European Molecular Biology Laboratory, Heidelberg, Germany; Max Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany

* To whom correspondence should be addressed.
Parantu K. Shah, E-mail: shah{at}embl.de


  Abstract

Motivation: Generation of alternative transcripts from the same gene in is an important biological event due to their contribution in creating functional diversity in eukaryotes. In this work, we choose the task of extracting information around this complex topic using a two step procedure involving machine learning and information extraction.

Results: In the first step, we trained a classifier that inductively learns to identify sentences about physiological transcript diversity from the MEDLINE abstracts. Using a large hand-built corpus, we compared the sentence classification performance of various text categorization methods. Support vector machines (SVM) followed by the maximum entropy classifier outperformed other methods for the sentence classification task. The SVM with the radial basis function kernel and optimized parameters achieved F{beta}-measure of 91% during the four-fold cross validation and of 74% when applied to all sentences in more than 12 million abstracts of MEDLINE. In the second step, we identified eight frequently present semantic categories in the sentences and performed a limited amount of semantic role labeling. The role labeling step also achieved very high F{beta}-measure for all eight categories.

Availability: The results of our two-step procedure are summarized in the LSAT database of alternative transcripts. LSAT is available at http://www.bork.embl.de/LSAT/.

Associate Editor: Chris Stoeckert
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