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Nucleic Acids Research 2005 33(Web Server Issue):W779-W782; doi:10.1093/nar/gki417
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts

Holger Maier, Stefanie Döhr, Korbinian Grote, Sean O'Keeffe, Thomas Werner, Martin Hrabé de Angelis and Ralf Schneider*

GSF-National Research Center for Environment and Health, Institute of Experimental Genetics, AG BIODV Ingolstädter Landstrasse 1, D-85768 Neuherberg, Germany

*To whom correspondence should be addressed. Tel: +49 89 3187 4060; Fax: +49 89 3187 4400; Email: ralf.schneider{at}gsf.de

Received February 12, 2005. Revised March 21, 2005. Accepted March 21, 2005.

The LitMiner software is a literature data-mining tool that facilitates the identification of major gene regulation key players related to a user-defined field of interest in PubMed abstracts. The prediction of gene-regulatory relationships is based on co-occurrence analysis of key terms within the abstracts. LitMiner predicts relationships between key terms from the biomedical domain in four categories (genes, chemical compounds, diseases and tissues). Owing to the limitations (no direction, unverified automatic prediction) of the co-occurrence approach, the primary data in the LitMiner database represent postulated basic gene–gene relationships. The usefulness of the LitMiner system has been demonstrated recently in a study that reconstructed disease-related regulatory networks by promoter modelling that was initiated by a LitMiner generated primary gene list. To overcome the limitations and to verify and improve the data, we developed WikiGene, a Wiki-based curation tool that allows revision of the data by expert users over the Internet. LitMiner (http://andromeda.gsf.de/litminer) and WikiGene (http://andromeda.gsf.de/wiki) can be used unrestricted with any Internet browser.

Present addresses: Korbinian Grote and Thomas Werner, Genomatrix Software GmbH, Landsberger Straße 6, D-80339 München, Germany


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