IC4R (Information Commons for Rice) is a curated knowledgebase for the research community, dedicating to provide rice reference genome with standardized and accurate gene annotations based on a huge volume of omics data and a large number of rice-related literatures. IC4R utilizes a Web Service-based architecture, which integrates data from multiple IC4R committed projects (Rice Expression Database, Rice Variation Database, Plant Homolog Database, Literature Miner, RiceWiki) through Web Application Programming Interfaces, thus bearing the potential to ease data integration, reusability, scalability, integrity, and community intelligence for collaborative knowledge curation.
Rice Expression Database (RED), a sub-project of IC4R, integrates expression profiles derived entirely from NGS RNA-Seq data of Nipponbare (Oryza Sativa japonica). RED includes RNA-seq data exclusively, providing information on gene expression profiles of normal tissues as well as tissues under a wide range of treatments. It provides friendly web interfaces for querying and visualizing gene expression profiles under different tissues and treatments.
Rice Variation Database is a database that contains 8,317,453 Single Nucleotide Polymorphisms (SNPs) of 5524 rice cultivars all over the world.
Plant Homolog Database (PHD) is a database composed of plant homologous genes. It combines phylogenetic and heuristic best-match approaches, yielding an accurate collection of more than 14,000 homologous groups covering multiple different species (including rice, Arabidopsis thaliana, tomato, maize, sorghum, etc). PHD provides highly interactive visualizations of multiple sequence alignment, phylogenetic tree, natural selection at each tree node/branch site, and duplication/speciation events which can be used for inference of ortholog, in-paralogs and out-paralogs.
Rice Literature Miner helps users find publications about rice and the genes within each article, which improves the productivity of curation (collecting and organizing information from publications).
RiceWiki is a subproject of IC4R (Information Commmons for Rice) as well as a component of ScienceWikis, is a wiki-based, publicly editable and open-content platform for community curation of rice genes, viz., a community-curated resource of rice knowledge. Unlike conventional biological databases based on expert curation, RiceWiki harnesses collective intelligence to collect, edit and annotate information about rice, quantifies users' contributions in each annotated gene and provides explicit authorship for each contributor to encourage more participation from the whole scientific community.