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      Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021

      research-article
      CNCB-NGDC Members and Partners
      Nucleic Acids Research
      Oxford University Press

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          Abstract

          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.

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          Most cited references40

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          Basic local alignment search tool.

          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            NCBI GEO: archive for functional genomics data sets—update

            The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats. GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data. This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data.
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              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              The EMBL-EBI search and sequence analysis tools APIs in 2019

              Abstract The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval capabilities. Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBL-EBI+Web+Services+APIs+-+Data+Retrieval). Both systems have been developed with the same core principles that allow them to integrate an ever-increasing volume of biological data, making them an integral part of many popular data resources provided at the EMBL-EBI. Here, we describe the latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                08 January 2021
                11 November 2020
                11 November 2020
                : 49
                : D1
                : D18-D28
                Author notes
                To whom correspondence should be addressed. Tel: +86 10 84097261; Fax: +86 10 84097720; Email: ybxue@ 123456big.ac.cn
                Correspondence may also be addressed to Yiming Bao. Email: baoym@ 123456big.ac.cn
                Correspondence may also be addressed to Zhang Zhang. Email: zhangzhang@ 123456big.ac.cn
                Correspondence may also be addressed to Wenming Zhao. Email: zhaowm@ 123456big.ac.cn
                Correspondence may also be addressed to Jingfa Xiao. Email: xiaojingfa@ 123456big.ac.cn
                Correspondence may also be addressed to Shunmin He. Email: heshunmin@ 123456ibp.ac.cn
                Correspondence may also be addressed to Guoqing Zhang. Email: gqzhang@ 123456picb.ac.cn
                Correspondence may also be addressed to Yixue Li. Email: yxli@ 123456sibs.ac.cn
                Correspondence may also be addressed to Guoping Zhao. Email: gpzhao@ 123456sibs.ac.cn
                Correspondence may also be addressed to Runsheng Chen. Email: crs@ 123456ibp.ac.cn

                Full list is provided in the Appendix.

                Article
                gkaa1022
                10.1093/nar/gkaa1022
                7779035
                33175170
                fb9c2c7f-3ab9-47eb-b590-ade50260d7b5
                © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                : 16 October 2020
                : 13 October 2020
                : 14 September 2020
                Page count
                Pages: 11
                Funding
                Funded by: Chinese Academy of Sciences, DOI 10.13039/501100002367;
                Award ID: XDB38030200
                Award ID: XDA19050302
                Award ID: XDA19090116
                Award ID: XDA24040201
                Award ID: XDB38050300
                Award ID: XDB38030100
                Award ID: XDB38030400
                Award ID: XDA12030100
                Award ID: XDB38040300
                Award ID: 153F11KYSB20160008
                Award ID: 153D31KYSB20170121
                Award ID: XXH13505-05
                Award ID: KJZD-EW-L14
                Award ID: 2019104
                Award ID: 2018134
                Award ID: 2017141
                Funded by: National Key Research and Development Program of China, DOI 10.13039/501100012166;
                Award ID: 2019YFA0801801
                Award ID: 2018YFA0801405
                Award ID: 2018YFD1000505
                Award ID: 2018YFC2000100
                Award ID: 2018YFC1406902
                Award ID: 2018YFC0910400
                Award ID: 2018YFC0310602
                Award ID: 2018YFA0903700
                Award ID: 2018YFA0900704
                Award ID: 2017YFC1201200
                Award ID: 2017YFC0908405
                Award ID: 2017YFC0908404
                Award ID: 2017YFC0908403
                Award ID: 2017YFC0907505
                Award ID: 2017YFC0907503
                Award ID: 2017YFC0907502
                Award ID: 2016YFE0206600
                Award ID: 2016YFC0906403
                Award ID: 2016YFC0903003
                Award ID: 2016YFC0901904
                Award ID: 2016YFC0901903
                Award ID: 2016YFC0901702
                Award ID: 2016YFC0901604
                Award ID: 2016YFC0901603
                Award ID: 2016YFB0201702
                Award ID: 2016YFA0501704
                Funded by: National Natural Science Foundation of China, DOI 10.13039/501100001809;
                Award ID: 91731303
                Award ID: 81670462
                Award ID: 31970565
                Award ID: 31871328
                Award ID: 31871294
                Award ID: 31701117
                Award ID: 31970647
                Award ID: 31801104
                Award ID: 31771465
                Award ID: 31771410
                Award ID: 31771388
                Award ID: 31671360
                Award ID: 81701567
                Award ID: 31571358
                Award ID: 31525014
                Award ID: 1470330
                Award ID: 31961130380
                Award ID: 31711530221
                Award ID: 31771477
                Award ID: 31571366
                Award ID: 31822030
                Award ID: 31801113
                Award ID: 31801154
                Award ID: 31771458
                Award ID: 91940303
                Award ID: 91940306
                Award ID: 31661143031
                Award ID: 31730110
                Award ID: 31871281
                Award ID: 31970634
                Award ID: 31930021
                Award ID: 31970633
                Funded by: Genomics Data Center Construction of Chinese Academy of Sciences;
                Award ID: XXH-13514-0202
                Funded by: Fundamental Research Funds for the Central Universities, DOI 10.13039/501100012226;
                Award ID: 2019kfyRCPY043
                Funded by: UK Royal Society-Newton Advanced Fellowship;
                Award ID: NAF\R1\191094
                Funded by: Key Research Program of Frontier Sciences of the Chinese Academy of Sciences;
                Award ID: QYZDJ-SSW-SYS009
                Funded by: Key Technology Talent Program of the Chinese Academy of Sciences;
                Funded by: K. C. Wong Education Foundation, DOI 10.13039/501100012692;
                Funded by: National Key Research and Development Program, DOI 10.13039/501100012166;
                Award ID: SQ2017YFSF090210
                Funded by: China Postdoctoral Science Foundation, DOI 10.13039/501100002858;
                Award ID: 2019M652623
                Award ID: 2018M632830
                Award ID: ANSO-PA-2020-07
                Funded by: Ministry of Science and Technology, DOI 10.13039/100007225;
                Award ID: 2018FY10080002
                Funded by: National Science and Technology Basic Resources Investigation;
                Award ID: 2019FY100102
                Funded by: Key Research Program of the Chinese Academy of Sciences;
                Award ID: KFZD-SW-219-5
                Funded by: Zhangjiang special project of national innovation demonstration zone;
                Award ID: ZJ2018-ZD-013
                Categories
                AcademicSubjects/SCI00010
                Database Issue

                Genetics
                Genetics

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