Database Commons

a catalog of worldwide biological databases

Rice serves as both a staple for over half of the world's population and a model organism for plants of the grass family. Beijing Genomics Institute (BGI) has long been engaged in rice genomic research: sequencing, assembly, information analysis and integration. Such intensive research results in public releases and biological applications. In order to facilitate obtaining and operating on the rice genomic data, as well as to provide a genomic groundwork for comparative, functional or evolutionary research on important cereal crops, BGI has established and updated the Rice Information System (BGI-RIS V2), an integrated information resource and comparative analysis workbench for rice genomes. BGI-RIS V2 offers not only genomic sequences, which combine the genomic data of Oryza sativa L. ssp. indica (by BGI) with Oryza sativa L. ssp. japonica, but also most detailed annotation data, including genetic markers, Bacterial Artificial Chromosome (BAC) end sequences, gene contents, cDNAs, oligos, tiling arrays, repetitive elements, and genomic polymorphisms. As a basic platform, BGI-RIS V2 also offers graphical interfaces and a series of tools and services for gene finding, genomic alignment and genomic assembly. This database is available through the web server (http://rise.genomics.org.cn or http://rice.genomics.org.cn) and the File Transfer Protocol (FTP) server (ftp://ftp.genomics.org.cn/pub/database/rice).

Rice is a major food staple for the world's population and serves as a model species in cereal genome research. The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing, information analysis and biological research of the rice and other crop genomes. In order to facilitate the application of the rice genomic information and to provide a foundation for functional and evolutionary studies of other important cereal crops, we implemented our Rice Information System (BGI-RIS), the most up-to-date integrated information resource as well as a workbench for comparative genomic analysis. In addition to comprehensive data from Oryza sativa L. ssp. indica sequenced by BGI, BGI-RIS also hosts carefully curated genome information from Oryza sativa L. ssp. japonica and EST sequences available from other cereal crops. In this resource, sequence contigs of indica (93-11) have been further assembled into Mbp-sized scaffolds and anchored onto the rice chromosomes referenced to physical/genetic markers, cDNAs and BAC-end sequences. We have annotated the rice genomes for gene content, repetitive elements, gene duplications (tandem and segmental) and single nucleotide polymorphisms between rice subspecies. Designed as a basic platform, BGI-RIS presents the sequenced genomes and related information in systematic and graphical ways for the convenience of in-depth comparative studies (http://rise.genomics.org.cn/).