IC4R Information Commons for Rice

Overview

Rice (Oryza sativa) is not only an important model organism for monocot plants and cereals but also the most widely consumed staple food for a large part of the world's human population. With the increasing volume of various types of omics data, an integrated database incorporating rice omics data is of great significance for the rice research community.

Information Commons for Rice (IC4R) is a rice knowledgebase based on an extensible and sustainable architecture that achieves data integration through community-contributed modules. IC4R is designed for scalability and sustainability, integrating data from remote resources through web APIs and featuring collaborative integration of rice data from multiple committed modules and low costs for database update and maintenance.

News Update

IC4R tools update

• A built-in BLAST modular was implemented in IC4R for users to conduct sequence similarity search.(2018-04-22)
• The ID Conversion which provides cross retrieval between different annotation version: IC4R2.0, MSU7.0, RAP-DB is available at our website.(2018-05-07)

Rice Genome Annotation Updated (2018-03-27)

The reference genes sets of rice Oryza sativa (ssp. japonica) genome have been updated through the IC4R Genome Re-annotation Project based on large-scale integration of RNA-Seq evidence. Current annotation version IC4R-1.0 significantly updated rice gene models by enhancing the completeness of mRNAs and incorporating a large amount of novelly identified alternative spliced isoforms and long non-coding RNAs. IC4R 2.0 release include:

• Protein-coding Genes: 56,221
• Protein-coding Transcripts: 80,038
• Circular RNAs: 4,373
• LncRNA Transcripts: 6,259
• RNA-Seq Datasets: 1,503

IC4R Omics Portal Updates (2018-02-27)

Genome-Wide DNA methylomes data is available at the IC4R omics Portal, which now provides 5912058 gene methylation profiles for rice genes generated from six rice methylation sequencing projects.

How to Cite

Publication:

• Information Commons for Rice (IC4R). Nucleic Acids Res 2016. [PMID=26519466]
• Database Resources of the BIG Data Center in 2018. Nucleic Acids Res 2018.[PMID=29036542]
• Rice Expression Database (RED): an integrated RNA-Seq-derived gene expression database for rice. J Genet Genomics 2017. [PMID:28529082]

Committee and Advisory Board

Committee

• Zhang Zhang: Beijing Institute of Genomics, Chinese Academy of Sciences
• Songnian Hu: Beijing Institute of Genomics, Chinese Academy of Sciences
• Fei Chen: Beijing Institute of Genomics, Chinese Academy of Sciences
• Jingfa Xiao: Beijing Institute of Genomics, Chinese Academy of Sciences
• Wenming Zhao: Beijing Institute of Genomics, Chinese Academy of Sciences
• Xiangfeng Wang: China Agricultural University
• Hang He: Peking University
• Yu Xue: Huazhong University of Science and Technology
• Ling-Ling Chen: Huazhong Agricultural University

Advisory Board

• Yongbiao Xue: Beijing Institute of Genomics, Chinese Academy of Sciences
• Lihuang Zhu: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
• Jun Yu: Beijing Institute of Genomics, Chinese Academy of Sciences
• Zheng Wang: Yale University
• Donghui Li: TAIR, Stanford University
• Xiaodong Wang: WormBase, California Institute of Technology

Participating Institutions