CNGBdb：国家基因库生命大数据平台

doi:10.16288/j.yczz.20-080

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Hereditas(Beijing) ›› 2020, Vol. 42 ›› Issue (8): 799-809.doi: 10.16288/j.yczz.20-080

• Resource and Platform • Previous Articles Next Articles

CNGBdb: China National GeneBank DataBase

Fengzhen Chen¹, Lijin You¹, Fan Yang¹, Lina Wang¹, Xueqin Guo¹, Fei Gao¹, Cong Hua¹, Cong Tan¹, Lin Fang², Riqiang Shan³, Wenjun Zeng¹, Bo Wang¹, Ren Wang¹(), Xun Xu^1,^2,⁴(), Xiaofeng Wei¹()

^1. China National GeneBank, Shenzhen 518120, China
^2. BGI-Shenzhen, Shenzhen 518083, China
^3. MGI-Shenzhen, Shenzhen 518083, China
^4. Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, China

Received:2020-03-23 Revised:2020-05-23 Online:2020-08-20 Published:2020-06-01
Contact: Wang Ren,Xu Xun,Wei Xiaofeng E-mail:wangren@cngb.org;xuxun@genomics.cn;weixiaofeng@cngb.org
Supported by:
Supported by Guangdong Provincial Key Laboratory of Genome Read and Write No(2017B030301011)

Abstract

Abstract:

China National GeneBank DataBase (CNGBdb) is a data platform aiming to systematically archiving and sharing of multi-omics data in life science. As the service portal of Bio-informatics Data Center of the core structure, namely, "Three Banks and Two Platforms" of China National GeneBank (CNGB), CNGBdb has the advantages of rich sample resources, data resources, cooperation projects, powerful data computation and analysis capabilities. With the advent of high throughput sequencing technologies, research in life science has entered the big data era, which is in the need of closer international cooperation and data sharing. With the development of China's economy and the increase of investment in life science research, we need to establish a national public platform for data archiving and sharing in life science to promote the systematic management, application and industrial utilization. Currently, CNGBdb can provide genomic data archiving, information search engines, data management and data analysis services. The data schema of CNGBdb has covered projects, samples, experiments, runs, assemblies, variations and sequences. Until May 22, 2020, CNGBdb has archived 2176 research projects and more than 2221 TB sequencing data submitted by researchers globally. In the future, CNGBdb will continue to be dedicated to promoting data sharing in life science research and improving the service capability. CNGBdb website is: https://db.cngb.org/.

Key words: China National GenBank Database, data sharing, data archiving, omics data

Fengzhen Chen, Lijin You, Fan Yang, Lina Wang, Xueqin Guo, Fei Gao, Cong Hua, Cong Tan, Lin Fang, Riqiang Shan, Wenjun Zeng, Bo Wang, Ren Wang, Xun Xu, Xiaofeng Wei. CNGBdb: China National GeneBank DataBase[J]. Hereditas(Beijing), 2020, 42(8): 799-809.

Figures/Tables 5

Fig. 1

Table 1

Fig. 2

Table 2

Table 3

Some datasets created by CNGBdb users"

分类	数据集名称	简要介绍	网址
植物	10,000 Plant Genomes Project	万种植物基因组项目数据集	https://db.cngb.org/datamart/plant/DATApla1/
	The 3000 Rice Genomes Project	3000水稻项目数据集	https://db.cngb.org/datamart/plant/DATApla2/
	1000 Plant Transcriptomes	千种植物转录组项目数据集	https://db.cngb.org/datamart/plant/DATApla4/
	Data of Ruili Botanical Garden	瑞丽珍稀植物园689种植物基因组测序数据	https://db.cngb.org/datamart/plant/DATApla5/
动物	The B10K Genomes Project	万种鸟基因组项目数据集	https://db.cngb.org/datamart/animal/DATAani1/
	1K Insect Transcriptome	千种昆虫转录组数据集	https://db.cngb.org/datamart/animal/DATAani3/
	Transcriptomes of 1000 Fishes	千种鱼转录组数据集	https://db.cngb.org/datamart/animal/DATAani2/
	Vertebrate Genomes 10K	万种脊椎动物数据集	https://db.cngb.org/datamart/animal/DATAani5/
	Life Periodic Plan (LPP)	生命周期表项目数据集	https://db.cngb.org/datamart/animal/DATAani6/
微生物	1520 reference genomes	覆盖人体肠道中所有主要细菌门和属的1520个基因组数据集	https://db.cngb.org/datamart/microbe/DATAmic1/
	Earth Microbiome Project	地球微生物组项目数据集	https://db.cngb.org/datamart/microbe/DATAmic4/
	1000 Fungal Genomes Project	千种真菌基因组项目数据集	https://db.cngb.org/datamart/microbe/DATAmic7/
	MetaHIT (metagenomics of humanintestinal tract)	欧盟的肠道微生物组计划数据集	https://db.cngb.org/datamart/microbe/DATAmic5/
	Human Microbiome Project	人类微生物组项目数据集	https://db.cngb.org/datamart/microbe/DATAmic3/
人群	WGS of 175 Mongolians	175个蒙古人基因组数据集	https://db.cngb.org/datamart/other/DATAoth1/
人群	1000 Genomes Project (human)	千人基因组项目数据集	https://db.cngb.org/datamart/other/DATAoth2/

Table 3

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数据类型	索引量(万)	主要外源数据库	主要信息
文献	2947.19	GigaScience、PubMed和Europe PMC	文献标题、摘要、医学关键词、引用和参考文献和文献相关数据等
基因	2274.41	NCBI Gene	基因名称、染色体位置、基因产物和它的属性、基因所在的基因组、基因序列和基因变异等
变异	76323.01	dbSNP^[28]、dbVar和ClinVar^[29]	变异名称(HGVS名称)、基因组位置、相关物种、人群频率以及变异数据与疾病、表型和文献等
蛋白	13406.59	Uniprot^[30]	蛋白名称、蛋白长度、物种和编码蛋白的基因等
序列	213665.12	NCBI Refseq^[31]和GenBank^[8]	序列名称、序列长度、物种和fastq序列文件等
项目	35.63	NCBI BioProject^[32]	项目的名称、描述和数据类型等
样本	1007.36	NCBI BioSample^[8]	样本的名称、物种、样本类型和描述等
实验	5515.46	NCBI SRA^[33]	实验的题目、测序平台、文库构建策略、文库来源和文库选项等
组装	0.24	NCBI Assembly^[34]	组装的名称、分子类型、测序技术和组装方法等

数据源	数据库名称	数据库编号	数据库格式版本
CNGB	The 1000 Plants Project	onekp	v5
	Microbiome DataBase	microbiome	v5
	Pan Immune Repertoire Database	pird	v5
	The Transcriptomes of 1,000 Fishes Project	fisht1k	v5
	The Bird 10,000 Genomes Project	b10k	v5
NCBI	Nucleotide collection	nt	v5
	Reference proteins	refseq_protein	v4
	16S ribosomal RNA sequences	16smicrobial	v4
	Human genomic	human_genomic	v4
	RefSeq Representative genomes	refseq_representative_genomes	v4
	Non-human organisms genomic	other_genomic	v4
	Human RefSeqGene sequences	refseqgene	v4
	Genomic survey sequences	gss	v4
	Reference genomic sequences	refseq_genomic	v4
	High throughput genomic sequences	htgs	v4
	Transcriptome Shotgun Assembly	tsa	v4
	Expressed sequence tags	est	v4
	Patent sequences	pat	v4
	Sequence tagged sites	sts	v4
	Protein Data Bank	pdb	v4
	Metagenomic sequences	env	v4

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