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Nucleic Acids Research Advance Access published online on May 15, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn286
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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E3Miner: a text mining tool for ubiquitin-protein ligases

Hodong Lee1, Gwan-Su Yi2 and Jong C. Park1,*

1Department of Computer Science, KAIST, 335 Gwahangno, Yuseong-gu, Daejeon 305-701 and 2School of Engineering, Information and Communications University, 119 Munjiro, Yuseong-gu, Daejeon 305-732, South Korea

*To whom correspondence should be addressed. Tel: +82 42 869 3541; Fax: +82 42 869 5581; Email: park{at}nlp.kaist.ac.kr

Received February 20, 2008. Revised April 17, 2008. Accepted April 26, 2008.

Ubiquitination is a regulatory process critically involved in the degradation of >80% of cellular proteins, where such proteins are specifically recognized by a key enzyme, or a ubiquitin-protein ligase (E3). Because of this important role of E3s, a rapidly growing body of the published literature in biology and biomedical fields reports novel findings about various E3s and their molecular mechanisms. However, such findings are neither adequately retrieved by general text-mining tools nor systematically made available by such protein databases as UniProt alone. E3Miner is a web-based text mining tool that extracts and organizes comprehensive knowledge about E3s from the abstracts of journal articles and the relevant databases, supporting users to have a good grasp of E3s and their related information easily from the available text. The tool analyzes text sentences to identify protein names for E3s, to narrow down target substrates and other ubiquitin-transferring proteins in E3-specific ubiquitination pathways and to extract molecular features of E3s during ubiquitination. E3Miner also retrieves E3 data about protein functions, other E3-interacting partners and E3-related human diseases from the protein databases, in order to help facilitate further investigation. E3Miner is freely available through http://e3miner.biopathway.org.


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