Database Commons

a catalog of biological databases

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

Database information

IC4R (Information Commons for Rice)

General information

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:
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Country/Region: China
Data type:
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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

Record metadata

Created on: 2016-01-02
Curated by:
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]

Ranking

All databases:
1560/4549 (65.729%)
Expression:
293/800 (63.5%)
Interaction:
246/671 (63.487%)
Literature:
88/284 (69.366%)
Genotype phenotype and variation:
204/611 (66.776%)
Standard ontology and nomenclature:
82/182 (55.495%)
1560
Total Rank
15
Citations
3.75
z-index

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Publications

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) | 15 Citations (from Europe PMC, 2020-04-04)