Journal Article

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

Yuko Makita, Norio Kobayashi, Yoshiki Mochizuki, Yuko Yoshida, Satomi Asano, Naohiko Heida, Mrinalini Deshpande, Rinki Bhatia, Akihiro Matsushima, Manabu Ishii, Shuji Kawaguchi, Kei Iida, Kosuke Hanada, Takashi Kuromori, Motoaki Seki, Kazuo Shinozaki and Tetsuro Toyoda

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 50, issue 7, pages 1249-1259
Published in print July 2009 | ISSN: 0032-0781
Published online June 2009 | e-ISSN: 1471-9053 | DOI: http://dx.doi.org/10.1093/pcp/pcp086
PosMed-plus: An Intelligent Search Engine that Inferentially Integrates Cross-Species Information Resources for Molecular Breeding of Plants

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  • Biochemistry
  • Molecular and Cell Biology
  • Plant Sciences and Forestry

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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

Journal Article.  4826 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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