Database Commons

a catalog of biological databases

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

Database Profile

General information

URL: https://ngdc.cncb.ac.cn
Full name: National Genomics Data Center
Description: The National Genomics Data Center (formerly named as BIG Data Center) advances life & health sciences by providing open access to a variety of resources, with the aim to translate big data into big discoveries and support activities in both academia and industry.
Year founded: 2016
Last update: 2020-10-19
Version: v3.0
Accessibility:
Manual:
Accessible
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Country/Region: China

Contact information

University/Institution: Beijing Institute of Genomics, Chinese Academy of Sciences
Address: 1 Beichen West Road, Chaoyang District, Beijing 100101, China
City: Beijing
Province/State: Beijing
Country/Region: China
Contact name (PI/Team): Zhang Zhang
Contact email (PI/Helpdesk): zhangzhang@big.ac.cn

Publications

34718731
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. [PMID: 34718731]
null null

The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry. With the explosively accumulated multi-omics data at ever-faster rates, CNCB-NGDC is constantly scaling up and updating its core database resources through big data archive, curation, integration and analysis. In the past year, efforts have been made to synthesize the growing data and knowledge, particularly in single-cell omics and precision medicine research, and a series of resources have been newly developed, updated and enhanced. Moreover, CNCB-NGDC has continued to daily update SARS-CoV-2 genome sequences, variants, haplotypes and literature. Particularly, OpenLB, an open library of bioscience, has been established by providing easy and open access to a substantial number of abstract texts from PubMed, bioRxiv and medRxiv. In addition, Database Commons is significantly updated by cataloguing a full list of global databases, and BLAST tools are newly deployed to provide online sequence search services. All these resources along with their services are publicly accessible at https://ngdc.cncb.ac.cn.

Nucleic Acids Res. 2022:50(D1) | 7 Citations (from Europe PMC, 2022-05-14)
33175170
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. [PMID: 33175170]
CNCB-NGDC Members and Partners.

The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, updating and enriching its core database resources through big data deposition, integration and translation. In the past year, considerable efforts have been devoted to 2019nCoVR, a newly established resource providing a global landscape of SARS-CoV-2 genomic sequences, variants, and haplotypes, as well as Aging Atlas, BrainBase, GTDB (Glycosyltransferases Database), LncExpDB, and TransCirc (Translation potential for circular RNAs). Meanwhile, a series of resources have been updated and improved, including BioProject, BioSample, GWH (Genome Warehouse), GVM (Genome Variation Map), GEN (Gene Expression Nebulas) as well as several biodiversity and plant resources. Particularly, BIG Search, a scalable, one-stop, cross-database search engine, has been significantly updated by providing easy access to a large number of internal and external biological resources from CNCB-NGDC, our partners, EBI and NCBI. All of these resources along with their services are publicly accessible at https://bigd.big.ac.cn.

Nucleic Acids Res. 2021:49(D1) | 60 Citations (from Europe PMC, 2022-05-14)
34175476
Genome Warehouse: A Public Repository Housing Genome-scale Data. [PMID: 34175476]
Meili Chen, Yingke Ma, Song Wu, Xinchang Zheng, Hongen Kang, Jian Sang, Xingjian Xu, Lili Hao, Zhaohua Li, Zheng Gong, Jingfa Xiao Writing, Zhang Zhang, Wenming Zhao, Yiming Bao

The Genome Warehouse (GWH) is a public repository housing genome assembly data for a wide range of species and delivering a series of web services for genome data submission, storage, release, and sharing. As one of the core resources in the National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB, https://ngdc.cncb.ac.cn), GWH accepts both full genome and partial genome (chloroplast, mitochondrion, and plasmid) sequences with different assembly levels, as well as an update of existing genome assemblies. For each assembly, GWH collects detailed genome-related metadata of biological project, biological sample, and genome assembly, in addition to genome sequence and annotation. To archive high-quality genome sequences and annotations, GWH is equipped with a uniform and standardized procedure for quality control. Besides basic browse and search functionalities, all released genome sequences and annotations can be visualized with JBrowse. By May 21, 2021, GWH has received 19,124 direct submissions covering a diversity of 1108 species and has released 8772 of them. Collectively, GWH serves as an important resource for genome-scale data management and provides free and publicly accessible data to support research activities throughout the world. GWH is publicly accessible at https://ngdc.cncb.ac.cn/gwh.

Genomics Proteomics Bioinformatics. 2021:() | 10 Citations (from Europe PMC, 2022-05-14)
31702008
Database Resources of the National Genomics Data Center in 2020. [PMID: 31702008]
National Genomics Data Center Members and Partners.

The National Genomics Data Center (NGDC) provides a suite of database resources to support worldwide research activities in both academia and industry. With the rapid advancements in higher-throughput and lower-cost sequencing technologies and accordingly the huge volume of multi-omics data generated at exponential scales and rates, NGDC is continually expanding, updating and enriching its core database resources through big data integration and value-added curation. In the past year, efforts for update have been mainly devoted to BioProject, BioSample, GSA, GWH, GVM, NONCODE, LncBook, EWAS Atlas and IC4R. Newly released resources include three human genome databases (PGG.SNV, PGG.Han and CGVD), eLMSG, EWAS Data Hub, GWAS Atlas, iSheep and PADS Arsenal. In addition, four web services, namely, eGPS Cloud, BIG Search, BIG Submission and BIG SSO, have been significantly improved and enhanced. All of these resources along with their services are publicly accessible at https://bigd.big.ac.cn.

Nucleic Acids Res. 2020:48(D1) | 94 Citations (from Europe PMC, 2022-05-14)
30365034
Database Resources of the BIG Data Center in 2019. [PMID: 30365034]
BIG Data Center Members.

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of multi-omics data generated at unprecedented scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big data integration and value-added curation. Resources with significant updates in the past year include BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Science Wikis (a catalog of biological knowledge wikis for community annotations) and IC4R (Information Commons for Rice). Newly released resources include EWAS Atlas (a knowledgebase of epigenome-wide association studies), iDog (an integrated omics data resource for dog) and RNA editing resources (for editome-disease associations and plant RNA editosome, respectively). To promote biodiversity and health big data sharing around the world, the Open Biodiversity and Health Big Data (BHBD) initiative is introduced. All of these resources are publicly accessible at http://bigd.big.ac.cn.

Nucleic Acids Res. 2019:47(D1) | 50 Citations (from Europe PMC, 2022-05-14)
30716410
Database Resources in BIG Data Center: Submission, Archiving, and Integration of Big Data in Plant Science. [PMID: 30716410]
Song S, Zhang Z.
Mol Plant. 2019:12(3) | 1 Citations (from Europe PMC, 2022-05-14)
29036542
Database Resources of the BIG Data Center in 2018. [PMID: 29036542]
BIG Data Center Members.

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. ? The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2018:46(D1) | 56 Citations (from Europe PMC, 2022-05-14)
27899658
The BIG Data Center: from deposition to integration to translation. [PMID: 27899658]
BIG Data Center Members.

Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations. The BIG Data Center is dedicated to constructing and maintaining biological databases through big data integration and value-added curation, conducting basic research to translate big data into big knowledge and providing freely open access to a variety of data resources in support of worldwide research activities in both academia and industry. All of these resources are publicly available and can be found at http://bigd.big.ac.cn.

Nucleic Acids Res. 2017:45(D1) | 71 Citations (from Europe PMC, 2022-05-14)

Ranking

All databases:
148/5177 (97.161%)
Gene genome and annotation:
60/1407 (95.807%)
Raw bio-data:
14/510 (97.451%)
148
Total Rank
349
Citations
69.8
z-index

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Record metadata

Created on: 2017-01-09
Curated by:
Jing Wei [2022-04-19]
Zhang Zhang [2022-04-17]
Dong Zou [2021-06-27]
Zhang Zhang [2020-11-24]
Zhang Zhang [2020-10-28]
Zhang Zhang [2020-07-21]
Dong Zou [2020-01-25]
Zhang Zhang [2019-11-12]
Dong Zou [2019-11-11]
Lina Ma [2019-07-29]
Zhang Zhang [2018-11-28]
Zhang Zhang [2018-09-05]
Dong Zou [2018-03-05]
Dong Zou [2017-11-20]
lin liu [2017-11-06]
Zhang Zhang [2017-06-29]
Shixiang Sun [2017-02-08]
Zhang Zhang [2017-01-09]