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Plant and Cell Physiology Advance Access originally published online on June 15, 2009
Plant and Cell Physiology 2009 50(7):1249-1259; doi:10.1093/pcp/pcp086
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© The Author 2009. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. 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 the Japanese Society of Plant Physiologists 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@oxfordjournals.org

This article appears in the following Plant and Cell Physiology issue: Special Issue Articles: Omics and Bioinformatics [View the issue table of contents]

Special Issue - Regular Paper

PosMed-plus: An Intelligent Search Engine that Inferentially Integrates Cross-Species Information Resources for Molecular Breeding of Plants

Yuko Makita1,3, Norio Kobayashi1,3, Yoshiki Mochizuki1, Yuko Yoshida1, Satomi Asano1, Naohiko Heida1, Mrinalini Deshpande1, Rinki Bhatia1, Akihiro Matsushima1, Manabu Ishii1, Shuji Kawaguchi1, Kei Iida1, Kosuke Hanada2, Takashi Kuromori2, Motoaki Seki2, Kazuo Shinozaki2 and Tetsuro Toyoda1,*

1Bioinformatics And Systems Engineering (BASE) division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
2Plant Science Center (PSC), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan

*Corresponding author: E-mail, toyoda{at}base.riken.jp; Fax: +81-45-503-9553.


  Abstract

Molecular breeding of crops is an efficient way to upgrade plant functions useful to mankind. A key step is forward genetics or positional cloning to identify the genes that confer useful functions. In order to accelerate the whole research process, we have developed an integrated database system powered by an intelligent data-retrieval engine termed PosMed-plus (Positional Medline for plant upgrading science), allowing us to prioritize highly promising candidate genes in a given chromosomal interval(s) of Arabidopsis thaliana and rice, Oryza sativa. By inferentially integrating cross-species information resources including genomes, transcriptomes, proteomes, localizomes, phenomes and literature, the system compares a user’s query, such as phenotypic or functional keywords, with the literature associated with the relevant genes located within the interval. By utilizing orthologous and paralogous correspondences, PosMed-plus efficiently integrates cross-species information to facilitate the ranking of rice candidate genes based on evidence from other model species such as Arabidopsis. PosMed-plus is a plant science version of the PosMed system widely used by mammalian researchers, and provides both a powerful integrative search function and a rich integrative display of the integrated databases. PosMed-plus is the first cross-species integrated database that inferentially prioritizes candidate genes for forward genetics approaches in plant science, and will be expanded for wider use in plant upgrading in many species.

Keywords: Omics - Omic space - Superbrain - Web application

Abbreviations: NER, named entity recognition; QTL, quantitative trait locus; RFLP, restriction fragment length polymorphism; SSR, simple sequence repeat.

3These authors contributed equally to this work.

(Received March 31, 2009; Accepted June 10, 2009)
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