Beijing Genomics Institute Rice Information System
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Beijing Genomics Institute Rice Information System
metasource: Fairsharing.org
version: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
BGI-RIS
metasource: Fairsharing.org
version: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
BGI-RISe - Beijing Genomics Institute Rice Information System
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
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Beijing Genomics Institute Rice Information System
metasource: Fairsharing.orgversion: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
BGI-RIS
metasource: Fairsharing.orgversion: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
BGI-RISe - Beijing Genomics Institute Rice Information System
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Other names: BGI-RIS, BGI-RISe - Beijing Genomics Institute Rice Information System
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Beijing Genomics Institute Rice Information System
metasource: Fairsharing.orgversion: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
BGI-RIS
metasource: Fairsharing.orgversion: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
BGI-RISe - Beijing Genomics Institute Rice Information System
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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In BGI-RIS, sequence contigs of Beijing indica and Syngenta japonica have been further assembled and anchored onto the rice chromosomes. The database has annotated the rice genomes for gene content, repetitive elements, and SNPs. Sequence polymorphisms between different rice subspecies have also been identified.
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In BGI-RIS, sequence contigs of Beijing indica and Syngenta japonica have been further assembled and anchored onto the rice chromosomes. The database has annotated the rice genomes for gene content, repetitive elements, and SNPs. Sequence polymorphisms between different rice subspecies have also been identified.
metasource: Fairsharing.orgversion: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
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.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://rise.genomics.org.cn/Webpage
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http://rise.genomics.org.cn/
metasource: Fairsharing.orgversion: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
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BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
PMID: 14681438
metasource: Fairsharing.org
version: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gks1225
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
PMID: 14681438
metasource: Fairsharing.org
version: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gks1225
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
PubMed citations: 57.
57 articles citing: BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
The Economic, Medical and Psychosocial Consequences of Whole Genome Sequencing for the Genetic Diagnosis of Patients With Intellectual Disability: The DEFIDIAG Study Protocol. PMID:35444683
Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice. PMID:33947059
Recalibration of mapping quality scores in Illumina short-read alignments improves SNP detection results in low-coverage sequencing data. PMID:33354434
Conserved Imprinted Genes between Intra-Subspecies and Inter-Subspecies Are Involved in Energy Metabolism and Seed Development in Rice. PMID:33348666
RiceRelativesGD: a genomic database of rice relatives for rice research. PMID:31560050
Accelerating public sector rice breeding with high-density KASP markers derived from whole genome sequencing of indica rice. PMID:29563850
Comparative transcriptome analysis reveals molecular response to salinity stress of salt-tolerant and sensitive genotypes of indica rice at seedling stage. PMID:29391416
Identification of four functionally important microRNA families with contrasting differential expression profiles between drought-tolerant and susceptible rice leaf at vegetative stage. PMID:26369665
Profiling the expression domains of a rice-specific microRNA under stress. PMID:26029232
RiceNet v2: an improved network prioritization server for rice genes. PMID:25813048
Genome and metagenome sequencing: Using the human methyl-binding domain to partition genomic DNA derived from plant tissues. PMID:25383266
Genetic analysis of ion-beam induced extremely late heading mutants in rice. PMID:25320557
Gramene 2013: comparative plant genomics resources. PMID:24217918
RiceWiki: a wiki-based database for community curation of rice genes. PMID:24136999
STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice. PMID:23314754
OrysPSSP: a comparative platform for small secreted proteins from rice and other plants. PMID:23203890
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. PMID:23193278
Identification of genome-wide variations among three elite restorer lines for hybrid-rice. PMID:22383984
Analysis of trehalose-6-phosphate synthase (TPS) gene family suggests the formation of TPS complexes in rice. PMID:21598083
Rice-Map: a new-generation rice genome browser. PMID:21450055
Analyses of phylogeny, evolution, conserved sequences and genome-wide expression of the ICK/KRP family of plant CDK inhibitors. PMID:21385782
Plant noncoding RNA gene discovery by "single-genome comparative genomics". PMID:21220549
Identification and analysis of seven H₂O₂-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica). PMID:21113019
Gramene database in 2010: updates and extensions. PMID:21076153
RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles. PMID:20860998
PlnTFDB: updated content and new features of the plant transcription factor database. PMID:19858103
MyBASE: a database for genome polymorphism and gene function studies of Mycobacterium. PMID:19228437
Genomic and genetic database resources for the grasses. PMID:19126704
Bioinformatics in China: a personal perspective. PMID:18437216
Analysis of 142 genes resolves the rapid diversification of the rice genus. PMID:18315873
The Rice Annotation Project Database (RAP-DB): 2008 update. PMID:18089549
Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PMID:18043742
Gramene: a growing plant comparative genomics resource. PMID:17984077
A genome-wide gain-of function analysis of rice genes using the FOX-hunting system. PMID:17929174
MethyCancer: the database of human DNA methylation and cancer. PMID:17890243
A BAC end view of the Musa acuminata genome. PMID:17562019
A genome-wide microsatellite polymorphism database for the indica and japonica rice. PMID:17452422
Rice functional genomics research in China. PMID:17347106
A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China. PMID:17331896
Improvement of whole-genome annotation of cereals through comparative analyses. PMID:17284677
Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. PMID:17225073
The TIGR Rice Genome Annotation Resource: improvements and new features. PMID:17145706
PigGIS: Pig Genomic Informatics System. PMID:17090590
Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. PMID:17065465
Neighboring-nucleotide effects on the mutation patterns of the rice genome. PMID:16487081
Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes. PMID:16448571
Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice. PMID:16381819
Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. PMID:16284311
A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray. PMID:16217608
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. PMID:16140994
Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. PMID:15960804
DNA rearrangement in orthologous orp regions of the maize, rice and sorghum genomes. PMID:15834137
The Genomes of Oryza sativa: a history of duplications. PMID:15685292
Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics. PMID:15608281
ChickVD: a sequence variation database for the chicken genome. PMID:15608233
SilkDB: a knowledgebase for silkworm biology and genomics. PMID:15608225
An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. PMID:15342564 - http://dx.doi.org/10.1093/nar/gks1225
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biological regulation
metasource: Fairsharing.org
version: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
single nucleotide polymorphism
metasource: Fairsharing.org
version: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
plant databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
rice
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
biological regulation
metasource: Fairsharing.orgversion: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
deoxyribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
single nucleotide polymorphism
metasource: Fairsharing.orgversion: FAIRsharing.org: BGI-RIS; Beijing Genomics Institute Rice Information System; DOI: https://doi.org/10.25504/FAIRsharing.gk7nfn; Last edited: Jan. 8, 2019, 1:16 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
plant databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
rice
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
biological regulation dna single nucleotide polymorphism plant rice
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