title: CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes.
abstract: To understand newly sequenced genomes of closely related species, comprehensively curated reference genome databases are becoming increasingly important. We have extended CyanoBase (http://genome.microbedb.jp/cyanobase), a genome database for cyanobacteria, and newly developed RhizoBase (http://genome.microbedb.jp/rhizobase), a genome database for rhizobia, nitrogen-fixing bacteria associated with leguminous plants. Both databases focus on the representation and reusability of reference genome annotations, which are continuously updated by manual curation. Domain experts have extracted names, products and functions of each gene reported in the literature. To ensure effectiveness of this procedure, we developed the TogoAnnotation system offering a web-based user interface and a uniform storage of annotations for the curators of the CyanoBase and RhizoBase databases. The number of references investigated for CyanoBase increased from 2260 in our previous report to 5285, and for RhizoBase, we perused 1216 references. The results of these intensive annotations are displayed on the GeneView pages of each database. Advanced users can also retrieve this information through the representational state transfer-based web application programming interface in an automated manner.
authors.affiliation: Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan, Database Center for Life Science, Research Organization of Information and Systems, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan, Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan and Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan.
authors.forename: Takatomo
authors.initials: T
authors.lastname: Fujisawa
authors.forename: Shinobu
authors.initials: S
authors.lastname: Okamoto
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Katayama
authors.forename: Mitsuteru
authors.initials: M
authors.lastname: Nakao
authors.forename: Hidehisa
authors.initials: H
authors.lastname: Yoshimura
authors.forename: Hiromi
authors.initials: H
authors.lastname: Kajiya-Kanegae
authors.forename: Sumiko
authors.initials: S
authors.lastname: Yamamoto
authors.forename: Chiyoko
authors.initials: C
authors.lastname: Yano
authors.forename: Yuka
authors.initials: Y
authors.lastname: Yanaka
authors.forename: Hiroko
authors.initials: H
authors.lastname: Maita
authors.forename: Takakazu
authors.initials: T
authors.lastname: Kaneko
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tabata
authors.forename: Yasukazu
authors.initials: Y
authors.lastname: Nakamura
mesh_terms: D020561:Alphaproteobacteria / Q000235:genetics*; D020369:Bradyrhizobium / Q000235:genetics; D000458:Cyanobacteria / Q000235:genetics*; D030541:Databases, Genetic; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D020407:Internet; D059128:Mesorhizobium / Q000235:genetics; D058977:Molecular Sequence Annotation; D012231:Rhizobium / Q000235:genetics; D020579:Sinorhizobium / Q000235:genetics