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. 2024 Jan 5;52(D1):D18-D32.
doi: 10.1093/nar/gkad1078.

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024

CNCB-NGDC Members and Partners
Collaborators

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024

CNCB-NGDC Members and Partners. Nucleic Acids Res. .

Abstract

The National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support the global academic and industrial communities. With the rapid accumulation of multi-omics data at an unprecedented pace, CNCB-NGDC continuously expands and updates core database resources through big data archiving, integrative analysis and value-added curation. Importantly, NGDC collaborates closely with major international databases and initiatives to ensure seamless data exchange and interoperability. Over the past year, significant efforts have been dedicated to integrating diverse omics data, synthesizing expanding knowledge, developing new resources, and upgrading major existing resources. Particularly, several database resources are newly developed for the biodiversity of protists (P10K), bacteria (NTM-DB, MPA) as well as plant (PPGR, SoyOmics, PlantPan) and disease/trait association (CROST, HervD Atlas, HALL, MACdb, BioKA, BioKA, RePoS, PGG.SV, NAFLDkb). All the resources and services are publicly accessible at https://ngdc.cncb.ac.cn.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
The core database resources of CNCB-NGDC organized into various categories. These database resources are publicly accessible and searchable through CNCB-NGDC home page at https://ngdc.cncb.ac.cn. A full list of data resources is shown at https://ngdc.cncb.ac.cn/databases.
Figure 2.
Figure 2.
The connectivity of CNCB-NGDC core databases. BioProject, GSA-human and GVM are closely interconnected through a BioProject ID (e.g. PRJCA004209), allowing users to easily navigate between databases and access related information including biological project (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA004209), genomic information (https://ngdc.cncb.ac.cn/gsa-human/browse/HRA001552) and genetic variation (https://ngdc.cncb.ac.cn/gvm/getProjectDetail?project=GVM000115). Based on these information, users can further find a wealth of knowledge about any specific gene, taking TP53 for example, such as its epigenetic associations in EWAS Atlas (https://ngdc.cncb.ac.cn/ewas/browse?gene=TP53), transcriptional associations in TWAS Atlas (https://ngdc.cncb.ac.cn/twas/genedetail/ENSG00000141510.16), and cancer-associated splicing events in ASCancer Atlas (https://ngdc.cncb.ac.cn/ascancer/search?genename=TP53).
Figure 3.
Figure 3.
Statistics of data submissions to CNCB-NGDC. (A) Data statistics of BioProject and BioSample. (B) Data statistics of Experiments and Runs in GSA. (C) Timeline of data growth in GSA. (D) Statistics of genome assemblies in GWH. All statistics are regularly updated and publicly accessible at https://ngdc.cncb.ac.cn/bioproject, https://ngdc.cncb.ac.cn/biosample and https://ngdc.cncb.ac.cn/gsa and https://ngdc.cncb.ac.cn/gwh.
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