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Bioinformatics Advance Access originally published online on January 12, 2006
Bioinformatics 2006 22(7):857-865; 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

LSAT: learning about alternative transcripts in MEDLINE

Parantu K. Shah 1,2,* and Peer Bork 1,2

1European Molecular Biology Laboratory Heidelberg, Germany
2Max Delbrück Centre for Molecular Medicine Berlin-Buch, Germany

*To whom correspondence should be addressed at European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany

Motivation: Generation of alternative transcripts from the same gene 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 (SVMs) 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 Fß-measure of 91% during the 4-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 Fß-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

Contact: shah{at}embl.de

Supplementary information: Supplementary data are available at Bioinformatics online

Received on October 20, 2005; revised on December 9, 2005; accepted on January 5, 2006

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