遗传 ›› 2020, Vol. 42 ›› Issue (8): 799-809.doi: 10.16288/j.yczz.20-080
陈凤珍1, 游丽金1, 杨帆1, 王丽娜1, 郭学芹1, 高飞1, 华聪1, 谈聪1, 方林2, 单日强3, 曾文君1, 王博1, 王韧1(), 徐讯1,2,4(), 魏晓锋1()
收稿日期:
2020-03-23
修回日期:
2020-05-23
出版日期:
2020-08-20
发布日期:
2020-06-01
通讯作者:
王韧,徐讯,魏晓锋
E-mail:wangren@cngb.org;xuxun@genomics.cn;weixiaofeng@cngb.org
作者简介:
陈凤珍,本科,研究方向:生物大数据。E-mail: 基金资助:
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 Xu1,2,4(), Xiaofeng Wei1()
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:
摘要:
国家基因库生命大数据平台(China National GeneBank DataBase, CNGBdb)是一个致力于生命科学多组学数据归档和开放共享的数据库平台,是深圳国家基因库的核心功能“三库两平台”中生物信息数据库的对外服务平台,拥有深圳国家基因库丰富的样本资源、数据资源、合作项目资源和强大的数据计算和分析能力等优势。生命科学研究已经进入到了一个以高通量多组学数据为基础的大数据时代,迫切需要加强国际合作和信息共享。随着中国经济的发展和在生命科学研究领域的研究项目投入力度的加大,需要建立相关的生命大数据归档和共享的平台, 来促进我国生命科学研究项目中生成的基因组学数据的系统管理、开放共享与合理利用。目前,CNGBdb主要提供生命科学研究相关的数据归档、知识搜索、数据管理、数据计算和数据服务等服务。其归档和共享的数据类型,主要包括项目、样本、实验、测序、组装、变异、序列等。截止2020年5月22号, CNGBdb已接受了全球生命科学科研工作者提交的研究项目达2176个,归档的基因组学数据量超过2221 TB。未来,CNGBdb将继续推动生命科学研究多组学数据的开放共享和产业应用,完善基因组学数据的归档和共享功能,提升其服务生命科学数据开放共享的能力。CNGBdb的网址是:https://db.cngb.org/。
陈凤珍, 游丽金, 杨帆, 王丽娜, 郭学芹, 高飞, 华聪, 谈聪, 方林, 单日强, 曾文君, 王博, 王韧, 徐讯, 魏晓锋. CNGBdb:国家基因库生命大数据平台[J]. 遗传, 2020, 42(8): 799-809.
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.
表1
知识搜索服务数据"
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[ | 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[ | 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[ | 序列名称、序列长度、物种和fastq序列文件等 |
项目 | 35.63 | NCBI BioProject[ | 项目的名称、描述和数据类型等 |
样本 | 1007.36 | NCBI BioSample[ | 样本的名称、物种、样本类型和描述等 |
实验 | 5515.46 | NCBI SRA[ | 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[ | 组装的名称、分子类型、测序技术和组装方法等 |
表2
BLAST工具数据资源"
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 |
表3
CNGBdb用户已创建的部分数据集"
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/ |
1000 Genomes Project (human) | 千人基因组项目数据集 | https://db.cngb.org/datamart/other/DATAoth2/ |
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