The international nucleotide sequence database collaboration
Open accessAbstract
For more than 30 years, the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org/) has been committed to capturing, preserving and providing access to comprehensive public domain nucleotide sequence and associated metadata which enables discovery in biomedicine, biodiversity and biological sciences. Since 1987, the DNA Data Bank of Japan (DDBJ) at the National Institute for Genetics in Mishima, Japan; the European Nucleotide Archive (ENA) at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK; and GenBank at National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health in Bethesda, Maryland, USA have worked collaboratively to enable access to nucleotide sequence data in standardized formats for the worldwide scientific community. In this article, we reiterate the principles of the INSDC collaboration and briefly summarize the trends of the archival content.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Through partnership with ENA, sequencing data and metadata submitted for analysis are accessioned and stored permanently within the archive, which operates under INSDC.
“Through partnership with the ENA, sequencing data and metadata submitted for analysis are accessioned and stored permanently within the archive, which operates under the International Nucleotide Sequence Database Collaboration (INSDC) (15).”
From MGnify: the microbiome analysis resource in 2020 (2019) · cites this paper as [15]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
The FAIR Guiding Principles for scientific data management and stewardship
Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.18 · Cited by 18,423 · see citing works
Federhen, S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1178 · Cited by 1,436 · see citing works
Yilmaz, P., Kottmann, R., Field, D., Knight, R. D., Cole, J. R., Amaral‐Zettler, L., Gilbert, J. A., Karsch‐Mizrachi, I., Johnston, A., Cochrane, G., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1823 · Cited by 802 · see citing works
Self-citationThe International Nucleotide Sequence Database Collaboration
Karsch‐Mizrachi, I., Nakamura, Y., & Cochrane, G. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1006 · Cited by 717 · see citing works
Self-citationBenson, D. A., Cavanaugh, M. L., Clark, K., Karsch‐Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1070 · Cited by 629 · see citing works
Self-citationNCBI’s Database of Genotypes and Phenotypes: dbGaP
Tryka, K. A., Hao, L., Sturcke, A., Jin, Y., Wang, Z. Y., Ziyabari, L., Lee, M., Popova, N. V., Sharopova, N., Kimura, M., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1211 · Cited by 531 · see citing works
A holistic approach to marine eco-systems biology
Karsenti, E., Acinas, S. G., Bork, P., Bowler, C., De Vargas, C., Raes, J., Sullivan, M., Arendt, D., Benzoni, F., Claverie, J.-M., et al. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001177 · Cited by 477 · see citing works
Allard, M. W., Strain, E. A., Melka, D. C., et al. (2016) · Journal of Clinical Microbiology · doi:10.1128/jcm.00081-16 · Cited by 369 · see citing works
The European Genome-phenome Archive of human data consented for biomedical research
Lappalainen, I., Almeida, J. P., Kumanduri, V., Senf, A., Spalding, D., Ur-Rehman, S., Saunders, G. I., Kandasamy, J., Cáccamo, M., Leinonen, R., et al. (2015) · Nature Genetics · doi:10.1038/ng.3312 · Cited by 359 · see citing works
The International Nucleotide Sequence Database Collaboration
Cochrane, G., Karsch‐Mizrachi, I., & Takagi, T. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1323 · Cited by 197 · see citing works
Self-citationType material in the NCBI Taxonomy Database
Federhen, S. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1127 · Cited by 185 · see citing works
Mashima, J., Kodama, Y., Fujisawa, T., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1001 · Cited by 101 · see citing works
European Nucleotide Archive in 2016
Toribio, A. L., Alako, B., Amid, C., Cerdeño-Tárraga, A. M., Clarke, L., Cleland, I., Fairley, S., Gibson, R., Goodgame, N., ten Hoopen, P., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1106 · Cited by 78 · see citing works
Self-citationA global coalition to sustain core data
Anderson, W. P. (2017) · Nature · doi:10.1038/543179a · Cited by 40 · see citing works
Genomic Standards Consortium Projects
Field, D., Sterk, P. J., Kottmann, R., et al. (2014) · Standards in Genomic Sciences · doi:10.4056/sigs.5559680 · Cited by 39 · see citing works
Genomic Standards Consortium Projects
Field, D., Sterk, P. J., Kottmann, R., et al. (2014) · Standards in Genomic Sciences · doi:10.4056/sigs.5559608 · Cited by 28 · see citing works
Reminder to deposit DNA sequences
Blaxter, M., Danchin, A., Savakis, B., Fukami-Kobayashi, K., Kurokawa, K., Sugano, S., Roberts, R. J., Salzberg, S. L., & Wu, C. (2016) · Science · doi:10.1126/science.aaf7672 · Cited by 27 · see citing works
Reminder to deposit DNA sequences
Salzberg, S. L. (2016) · Nature · doi:10.1038/533179a · Cited by 9 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
UniProt: a worldwide hub of protein knowledge
The UniProt Consortium (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1049 · Cited by 7,698 · see citing works
UniProt: the universal protein knowledgebase in 2021
The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1100 · Cited by 6,372 · see citing works
MGnify: the microbiome analysis resource in 2020
Mitchell, A. L., Almeida, A., Beracochea, M., Boland, M., Burgin, J., Cochrane, G., Crusoe, M. R., Kale, V., Potter, S. C., Richardson, L. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1035 · Cited by 562 · see citing works
Self-citationLightbody, G., Haberland, V., Browne, F., Taggart, L., Zheng, H., Parkes, E., & Blayney, J. K. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bby051 · Cited by 173 · see citing works
IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata
Camargo, A. P., Call, L., Roux, S., Nayfach, S., Huntemann, M., Palaniappan, K., Ratner, A., Chu, K., Mukherjeep, S., Reddy, T. B. K., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad964 · Cited by 87 · see citing works
Danchin, A., Ouzounis, C., Tokuyasu, T., & Zucker, J. (2018) · Microbial Biotechnology · doi:10.1111/1751-7915.13284 · Cited by 56 · see citing works
- Authors
- Karsch-Mizrachi, I., Takagi, T., Cochrane, G., & on behalf of the International Nucleotide Sequence Database Collaboration
- Affiliations
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- National Institute of Genetics (JP)
- European Bioinformatics Institute (GB)
- ORCID
- Cochrane, Guy
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-11-28
- Volume
- 46
- Issue
- D1
- Pages
- D48-D51
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC5753279
- OpenAlex
- W4252710376
- Cited by
- 190
- References
- 18
- Citations by year
- 2026: 8 · 2025: 9 · 2024: 13 · 2023: 17 · 2022: 22 · 2021: 27 · 2020: 40 · 2019: 27 · 2018: 26 · 2017: 1
- FWCI
- 50.88
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- European Bioinformatics Institute
- Topics
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- INSDC, DNA sequence databases, DDBJ, European Nucleotide Archive, GenBank, sequence metadata, data archiving, data access
- MeSH terms
- Animals, Classification, Europe, Humans, International Cooperation, Japan, National Library of Medicine (U.S.), United States, Databases, Factual, Computational Biology, Databases, Nucleic Acid, High-Throughput Nucleotide Sequencing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
