The extraction of enriched protein-protein interactions from biomedical text
BioNLP '07 Proceedings of the Workshop on BioNLP 2007: Biological, Translational, and Clinical Language Processing
Automatic Identification and Classification of Noun Argument Structures in Biomedical Literature
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
| Hi-index | 3.84 |
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 Fβ-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 Fβ-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@embl.de Supplementary information: Supplementary data are available at Bioinformatics online