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.
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:
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.