Database Commons

a catalog of biological databases

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

Database information

VCGDB (Virtual Chinese Genome Database)

General information

Description: Virtual Chinese Genome Database is a dynamic genome database of Chinese population. VCGDB is a big data solution based on public data released by 1000 Genomes Project.
Year founded: 2014
Last update: 2015-12-09
Version: v1.0
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: China
Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Beijing Institute of Genomics, Chinese Academy of Sciences
Address: No.1 Beichen West Road, Chaoyang District
City: Beijing
Province/State: Beijing
Country/Region: China
Contact name (PI/Team): Jingfa Xiao
Contact email (PI/Helpdesk): xiaojf@big.ac.cn

Record metadata

Created on: 2015-06-20
Curated by:
Dong Zou [2019-12-03]
Dong Zou [2019-01-04]
Hongyan Yin [2016-03-31]
Zhang Zhang [2016-02-06]
Zhang Zhang [2016-01-18]
Lin Liu [2016-01-03]
Lin Liu [2016-01-01]
Jian SA [2015-12-08]
Jian SA [2015-06-28]
Jian SA [2015-06-27]

Ranking

All databases:
3758/4656 (19.308%)
Gene genome and annotation:
1044/1237 (15.683%)
3758
Total Rank
4
Citations
0.667
z-index

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Word cloud

Publications

30465539
[Database resources of the reference genome and genetic variation maps for the Chinese population]. [PMID: 30465539]
Song S, Teng XF, Xiao JF.

With the implementation of the international human genome project and 1000 genome project, hundreds of Chinese individual genome sequences have been published. Establishing a high-precision Chinese population reference genome and identifying the unique genome variations are fundamental for future precision medicine research in China. To further meet the needs of scientific management and deep mining on the rapidly growing Chinese genomic data, Beijing Institute of Genomics, Chinese Academy of Sciences, has developed a Virtual Chinese Genome Database (VCGDB, http://bigd.big.ac.cn/vcg/) and Genome Variation Map (GVM, http://bigd.big.ac.cn/gvm/) based on the public whole genome sequencing data, which provides the worldwide services of data retrieval, sharing, downloading and online analysis. This paper presents the brief introduction of characteristics and functions of the two databases, as well as their future development and application prospects, aiming to provide useful information for the promotion and development of the reference genome and genome variation map database in China.

Yi Chuan. 2018:40(11) | 0 Citations (from Europe PMC, 2020-08-08)
24708222
VCGDB: a dynamic genome database of the Chinese population. [PMID: 24708222]
Ling Y, Jin Z, Su M, Zhong J, Zhao Y, Yu J, Wu J, Xiao J.

The data released by the 1000 Genomes Project contain an increasing number of genome sequences from different nations and populations with a large number of genetic variations. As a result, the focus of human genome studies is changing from single and static to complex and dynamic. The currently available human reference genome (GRCh37) is based on sequencing data from 13 anonymous Caucasian volunteers, which might limit the scope of genomics, transcriptomics, epigenetics, and genome wide association studies. We used the massive amount of sequencing data published by the 1000 Genomes Project Consortium to construct the Virtual Chinese Genome Database (VCGDB), a dynamic genome database of the Chinese population based on the whole genome sequencing data of 194 individuals. VCGDB provides dynamic genomic information, which contains 35 million single nucleotide variations (SNVs), 0.5 million insertions/deletions (indels), and 29 million rare variations, together with genomic annotation information. VCGDB also provides a highly interactive user-friendly virtual Chinese genome browser (VCGBrowser) with functions like seamless zooming and real-time searching. In addition, we have established three population-specific consensus Chinese reference genomes that are compatible with mainstream alignment software. VCGDB offers a feasible strategy for processing big data to keep pace with the biological data explosion by providing a robust resource for genomics studies; in particular, studies aimed at finding regions of the genome associated with diseases.

BMC Genomics. 2014:15() | 4 Citations (from Europe PMC, 2020-08-08)