Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Jan 6;53(D1):D49-D55.
doi: 10.1093/nar/gkae975.

The European Nucleotide Archive in 2024

Colman O'Cathail  1 , Alisha Ahamed  1 , Josephine Burgin  1 , Carla Cummins  1 , Rajkumar Devaraj  1 , Khadim Gueye  1 , Dipayan Gupta  1 , Vikas Gupta  1 , Muhammad Haseeb  1 , Maira Ihsan  1 , Eugene Ivanov  1 , Suran Jayathilaka  1 , Vishnukumar Kadhirvelu  1 , Manish Kumar  1 , Ankur Lathi  1 , Rasko Leinonen  1 , Jasmine McKinnon  1 , Lili Meszaros  1 , Joana Pauperio  1 , Stephane Pesant  1 , Nadim Rahman  1 , Gabriele Rinck  1 , Sandeep Selvakumar  1 , Swati Suman  1 , Yanisa Sunthornyotin  1 , Marianna Ventouratou  1 , Zahra Waheed  1 , Peter Woollard  1 , David Yuan  1 , Ahmad Zyoud  1 , Tony Burdett  1 , Guy Cochrane  1
Affiliations

The European Nucleotide Archive in 2024

Colman O'Cathail et al. Nucleic Acids Res. .

Abstract

The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena), maintained at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) provides freely accessible services, both for deposition of, and access to, open nucleotide sequencing data. Open scientific data are of paramount importance to the scientific community and contribute daily to the acceleration of scientific advance. Outlined here are changes to and updates on the ENA service in 2024, aligning with the broad goals of enhancing interoperability, globalisation of the service and scaling the platform to meet current and future needs.

PubMed Disclaimer

Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Graph showing growth in ENA submitted public and private data objects over the previous eight years. Suppressed, cancelled or killed objects are not included in the object counts. The ENA sees continual growth in all objects submitted. This graph does not include objects mirrored from INSDC partners.
Figure 2.
Figure 2.
Screenshot of a sample record in the ENA browser: https://www.ebi.ac.uk/ena/browser/view/SAMEA12788035. The right hand side red box presents the new sidebar menu item and the bottom red box presents the ORCID Data Claims section that appears once clicking on the sidebar menu.
Figure 3.
Figure 3.
Screenshot of a sample (https://www.ebi.ac.uk/ena/browser/view/SAMN06266124) ENA browser that displays the two sets of environmental tags (below the map) for a sample that was collected in the marine environment.
Figure 4.
Figure 4.
Diagram showing how tags from geolocation- and taxonomy-based evidence are used to assess if an ENA record likely originated from the marine environment with (H)igh, (M)edium or (L)ow confidence levels. (!) Cases where the two sets of evidence disagree can be used in order to investigate possible mistakes in the metadata. (X) Cases where there is no evidence that the record originated from the marine environment.
Figure 5.
Figure 5.
Screenshot of new data centric-view on a project record (https://www.ebi.ac.uk/ena/browser/view/PRJEB6603) from the ENA Browser. The new data focussed box is highlighted in red. Where no public data are available, this box displays a message indicating as such to the user. Traditionally, this would all be contained in the ‘general’ box, with no clear messaging about available public data.
Figure 6.
Figure 6.
Screenshot of the service health dashboard (https://www.ebi.ac.uk/ena/browser/service-status). This displays to users the name of the service, a description of what the service is responsible for and a live status using ‘UP’ or ‘DOWN’.
See this image and copyright information in PMC

References

    1. Yuan D., Ahamed A., Burgin J., Cummins C., Devraj R., Gueye K., Gupta D., Gupta V., Haseeb M., Ihsan M.et al. .. The European Nucleotide Archive in 2023. Nucleic Acids Res. 2023; 52:D92–D97. - PMC - PubMed
    1. Wilkinson M.D., Dumontier M., Aalbersberg I.J.J., Appleton G., Axton M., Baak A., Blomberg N., Boiten J.-W., da Silva Santos L.B., Bourne P.E.et al. .. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data. 2016; 3:160018. - PMC - PubMed
    1. Arita M., Karsch-Mizrachi I., Cochrane G.. The international nucleotide sequence database collaboration. Nucleic Acids Res. 2021; 49:D121–D124. - PMC - PubMed
    1. Sayers E.W., Cavanaugh M., Clark K., Pruitt K.D., Schoch C.L., Sherry S.T., Karsch-Mizrachi I.. GenBank. Nucleic Acids Res. 2021; 49:D92–D96. - PMC - PubMed
    1. Ogasawara O., Kodama Y., Mashima J., Kosuge T., Fujisawa T.. DDBJ Database updates and computational infrastructure enhancement. Nucleic Acids Res. 2020; 48:D45–D50. - PMC - PubMed

LinkOut - more resources