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Extraction of transcript diversity from scientific literature

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Item Type:Article
Title:Extraction of transcript diversity from scientific literature
Creators Name:Shah, P.K. and Jensen, L.J. and Boue, S. and Bork, P.
Abstract:Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered throughout the scientific literature. Thus, it is crucial to have a tool that can automatically extract the relevant facts and collect them in a knowledge base that can aid the interpretation of data from high-throughput methods. We have developed and applied a composite text-mining method for extracting information on transcript diversity from the entire MEDLINE database in order to create a database of genes with alternative transcripts. It contains information on tissue specificity, number of isoforms, causative mechanisms, functional implications, and experimental methods used for detection. We have mined this resource to identify 959 instances of tissue-specific splicing. Our results in combination with those from EST-based methods suggest that alternative splicing is the preferred mechanism for generating transcript diversity in the nervous system. We provide new annotations for 1,860 genes with the potential for generating transcript diversity. We assign the MeSH term "alternative splicing" to 1,536 additional abstracts in the MEDLINE database and suggest new MeSH terms for other events. We have successfully extracted information about transcript diversity and semiautomatically generated a database, LSAT, that can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression.
Source:PLoS Computational Biology
ISSN:1553-734X
Publisher:Public Library of Science (U.S.A.)
Volume:1
Number:1
Page Range:e10
Date:24 June 2005
Official Publication:https://doi.org/10.1371/journal.pcbi.0010010
PubMed:View item in PubMed

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