title: PosMed-plus: an intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants.
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.
authors.affiliation: Bioinformatics And Systems Engineering (BASE) division, RIKEN, Yokohama, Kanagawa, Japan.
authors.forename: Yuko
authors.initials: Y
authors.lastname: Makita
authors.forename: Norio
authors.initials: N
authors.lastname: Kobayashi
authors.forename: Yoshiki
authors.initials: Y
authors.lastname: Mochizuki
authors.forename: Yuko
authors.initials: Y
authors.lastname: Yoshida
authors.forename: Satomi
authors.initials: S
authors.lastname: Asano
authors.forename: Naohiko
authors.initials: N
authors.lastname: Heida
authors.forename: Mrinalini
authors.initials: M
authors.lastname: Deshpande
authors.forename: Rinki
authors.initials: R
authors.lastname: Bhatia
authors.forename: Akihiro
authors.initials: A
authors.lastname: Matsushima
authors.forename: Manabu
authors.initials: M
authors.lastname: Ishii
authors.forename: Shuji
authors.initials: S
authors.lastname: Kawaguchi
authors.forename: Kei
authors.initials: K
authors.lastname: Iida
authors.forename: Kosuke
authors.initials: K
authors.lastname: Hanada
authors.forename: Takashi
authors.initials: T
authors.lastname: Kuromori
authors.forename: Motoaki
authors.initials: M
authors.lastname: Seki
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Toyoda
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D018745:Genome, Plant; D016571:Neural Networks, Computer; D012275:Oryza / Q000235:genetics*; D014584:User-Computer Interface