Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://ic4r.org
Full name: Information Commons for Rice
Description: 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.
Year founded: 2015
Last update: 2018-08-19
Version: v2.0
Accessibility:
Manual:
Accessible
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Country/Region: China
Data type:
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Beijing Institute of Genomics, Chinese Academy of Sciences
Address: 1 Beichen West Road, Chaoyang District, Beijing 100101, China
City: Beijing
Province/State:
Country/Region: China
Contact name (PI/Team): Zhang Zhang
Contact email (PI/Helpdesk): zhangzhang@big.ac.cn

Publications

32683045
IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data. [PMID: 32683045]
Jian Sang, Dong Zou, Zhennan Wang, Fan Wang, Yuansheng Zhang, Lin Xia, Zhaohua Li, Lina Ma, Mengwei Li, Bingxiang Xu, Xiaonan Liu, Shuangyang Wu, Lin Liu, Guangyi Niu, Man Li, Yingfeng Luo, Songnian Hu, Lili Hao, Zhang Zhang

Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function. Although the availability of massive RNA-seq data provides great opportunities for gene model refinement, few efforts have been made to adopt these precious data in rice genome reannotation. Here we reannotate the rice (Oryza sativa L. ssp. japonica) genome based on integration of large-scale RNA-seq data and release a new annotation system IC4R-2.0. In general, IC4R-2.0 significantly improves the completeness of gene structure, identifies a number of novel genes, and integrates a variety of functional annotations. Furthermore, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are systematically characterized in the rice genome. Performance evaluation shows that compared to previous annotation systems, IC4R-2.0 achieves higher integrity and quality, primarily attributable to massive RNA-seq data applied in genome annotation. Consequently, we incorporate the improved annotations into the Information Commons for Rice (IC4R), a database integrating multiple omics data of rice, and accordingly update IC4R by providing more user-friendly web interfaces and implementing a series of practical online tools. Together, the updated IC4R, which is equipped with the improved annotations, bears great promise for comparative and functional genomic studies in rice and other monocotyledonous species. The IC4R-2.0 annotation system and related resources are freely accessible at http://ic4r.org/.

Genomics Proteomics Bioinformatics. 2020:() | 2 Citations (from Europe PMC, 2021-05-15)
26519466
Information Commons for Rice (IC4R). [PMID: 26519466]
IC4R Project Consortium, Hao L, Zhang H, Zhang Z, Hu S, Xue Y.

Rice is the most important staple food for a large part of the world's human population and also a key model organism for plant research. Here, we present Information Commons for Rice (IC4R; http://ic4r.org), a rice knowledgebase featuring adoption of an extensible and sustainable architecture that integrates multiple omics data through community-contributed modules. Each module is developed and maintained by different committed groups, deals with data collection, processing and visualization, and delivers data on-demand via web services. In the current version, IC4R incorporates a variety of rice data through multiple committed modules, including genome-wide expression profiles derived entirely from RNA-Seq data, resequencing-based genomic variations obtained from re-sequencing data of thousands of rice varieties, plant homologous genes covering multiple diverse plant species, post-translational modifications, rice-related literatures and gene annotations contributed by the rice research community. Unlike extant related databases, IC4R is designed for scalability and sustainability and thus also features collaborative integration of rice data and low costs for database update and maintenance. Future directions of IC4R include incorporation of other omics data and association of multiple omics data with agronomically important traits, dedicating to build IC4R into a valuable knowledgebase for both basic and translational researches in rice. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2016:44(D1) | 22 Citations (from Europe PMC, 2021-05-15)

Ranking

All databases:
1498/5039 (70.292%)
Expression:
277/915 (69.836%)
Interaction:
262/764 (65.838%)
Literature:
119/382 (69.11%)
Genotype phenotype and variation:
215/702 (69.516%)
Standard ontology and nomenclature:
82/203 (60.099%)
1498
Total Rank
24
Citations
4.8
z-index

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Record metadata

Created on: 2016-01-02
Curated by:
Ming Chen [2020-11-11]
Zhang Zhang [2018-11-28]
Zhang Zhang [2016-05-08]
Zhang Zhang [2016-01-08]
Zhang Zhang [2016-01-04]
lin liu [2016-01-02]