CNSA: a data repository for archiving omics data.

Yawen Yang,Bo Wan,Xueqin Guo,Lina Wang,Fei Gao,Chunhua Peng,Minwen Zhang,Bo Wang,Feiyu Zhou,Xiaofeng Wei,Zhiyong Li,Jiawei Tong,Lijin You,Wenjun Zeng,Linlin Yang,Fengzhen Chen,Jia Cai,Cong Hua,Ling Li,Xiaoxia Yang,Wanliang Liu,Lei Zhang,Ke Liu,Xun Xu,Tao Yang,Fan Yang

doi:10.1093/database/baaa055

Abstract

With the application and development of high-throughput sequencing technology in life and health sciences, massive multi-omics data brings the problem of efficient management and utilization. Database development and biocuration are the prerequisites for the reuse of these big data. Here, relying on China National GeneBank (CNGB), we present CNGB Sequence Archive (CNSA) for archiving omics data, including raw sequencing data and its further analyzed results which are organized into six objects, namely Project, Sample, Experiment, Run, Assembly and Variation at present. Moreover, CNSA has created a correlation model of living samples, sample information and analytical data on some projects. Both living samples and analytical data are directly correlated with the sample information. From either one, information or data of the other two can be obtained, so that all data can be traced throughout the life cycle from the living sample to the sample information to the analytical data. Complying with the data standards commonly used in the life sciences, CNSA is committed to building a comprehensive and curated data repository for storing, managing and sharing of omics data. We will continue to improve the data standards and provide free access to open-data resources for worldwide scientific communities to support academic research and the bio-industry.Database URL: https://db.cngb.org/cnsa/.

Highlights

In the data-intensive science era, life science research is seen as a data-driven, exploration-centered style of science
The International Nucleotide Sequence Database Collaboration (INSDC) [6] represents one of the most celebrated global initiatives in data and associated metadata sharing, which operates between DNA Data Bank of Japan (DDBJ) [7], the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) [8] and the National Center for Biotechnology Information (NCBI) [9]
We summarized the type and amount of sequence data archived in several sequence archive databases such as INSDC, the Cancer Genome Atlas (TCGA) and Genome Sequence Archive (GSA) [18] (Table 2), which will be helpful for the users when selecting specific databases for bioinformatics research

Summary

Introduction

In the data-intensive science era, life science research is seen as a data-driven, exploration-centered style of science. The UK’s 100 000 Genomes Project [1], the International Cancer Genome Consortium (ICGC) [2], the Cancer Genome Atlas (TCGA) [3], the China Kadoorie Biobank (CKB) [4] and Earth BioGenome Project (EBP) [5] have been announced or completed in the past decades. It poses great challenges in big data deposition, integration and sharing. In China, many scientific institutions have made great efforts and established multiple omics database systems such as the National Genomics Data Center (NGDC) [13], Bio-Med Big Data Center (BMDC: https://www.biosino. org/bmdc/index) and the National Center for Protein ScienceShanghai (NCPSS: http://www.sibcb-ncpss.org/ index.action)

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Conclusion