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Ensembl 2022

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Cunningham, Fiona, Allen, James E, Allen, Jamie, Alvarez-Jarreta, Jorge, Amode, M Ridwan, Armean, Irina M, Austine-Orimoloye, Olanrewaju, Azov, Andrey G +87 more·2022·Nucleic Acids Research
DOI 10.1093/nar/gkab1049PMC PMC8728283
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Abstract

Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.

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  • The impact of predicted structures is enhanced by their seamless integration into several core data resources, including PDBe-KB, UniProt, Ensembl, InterPro, Genecards and MobiDB.

    “The impact of the predicted structures is further enhanced by their seamless integration into several core data resources, including PDBe-KB (17), UniProt (6), Ensembl (16), InterPro (15), Genecards (24) and MobiDB (25), among others.”

    From AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences (2024) · cites this paper as [16]

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Authors
Cunningham, F., Allen, J. E., Allen, J., Alvarez-Jarreta, J., Amode, M. R., Armean, I. M., Austine-Orimoloye, O., Azov, A. G., Barnes, I., Bennett, R., Berry, A., Bhai, J., Bignell, A., Billis, K., Boddu, S., Brooks, L., Charkhchi, M., Cummins, C., Da Rin Fioretto, L., Davidson, C., Dodiya, K., Donaldson, S., El Houdaigui, B., El Naboulsi, T., Fatima, R., Giron, C. G., Genez, T., Martinez, J. G., Guijarro-Clarke, C., Gymer, A., Hardy, M., Hollis, Z., Hourlier, T., Hunt, T., Juettemann, T., Kaikala, V., Kay, M., Lavidas, I., Le, T., Lemos, D., Marugán, J. C., Mohanan, S., Mushtaq, A., Naven, M., Ogeh, D. N., Parker, A., Parton, A., Perry, M., Piližota, I., Prosovetskaia, I., Sakthivel, M. P., Salam, A. I. A., Schmitt, B. M., Schuilenburg, H., Sheppard, D., Pérez-Silva, J. G., Stark, W., Steed, E., Sutinen, K., Sukumaran, R., Sumathipala, D., Suner, M.-M., Szpak, M., Thormann, A., Tricomi, F. F., Urbina-Gómez, D., Veidenberg, A., Walsh, T. A., Walts, B., Willhoft, N., Winterbottom, A., Wass, E., Chakiachvili, M., Flint, B., Frankish, A., Giorgetti, S., Haggerty, L., Hunt, S. E., IIsley, G. R., Loveland, J. E., Martin, F. J., Moore, B., Mudge, J. M., Muffato, M., Perry, E., Ruffier, M., Tate, J., Thybert, D., Trevanion, S. J., Dyer, S., Harrison, P. W., Howe, K. L., Yates, A. D., Zerbino, D. R., & Flicek, P.
Affiliations
  • European Bioinformatics Institute (GB)
  • European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Corresponding author
Flicek, Paul
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2021-11-17
Volume
50
Issue
D1
Pages
D988-D995
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkab1049
PMC
PMC8728283
OpenAlex
W4200135473
Cited by
1,923
References
4
Citations by year
2026: 171 · 2025: 263 · 2024: 596 · 2023: 706 · 2022: 185 · 2021: 2
FWCI
122.75
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Wellcome Trust (WT108749/Z/15/Z, WT104947/Z/14/Z, WT200990/Z/16/Z, WT201535/Z/16/Z, WT108749/Z/15/A, WT212925/Z/18/Z, WT218328/B/19/Z)
  • National Human Genome Research Institute (U41HG007823, 2U41HG007234, U41HG010972, 2U24HG007497-05)
  • Biotechnology and Biological Sciences Research Council (BB/N019563/1, BB/M011615/1, BB/S020152/1, BB/P016855/1, BB/S02011X/1, BB/P024602/1)
  • British Council (414710385)
  • European Molecular Biology Laboratory
  • European Union's Horizon 2020 research and innovation programme (733161, 731060, 825575, 817923, 817998, 815668)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
Keywords
Ensembl, genome annotation, comparative genomics, vertebrate genomes, genomic data infrastructure
MeSH terms
Animals, Humans, Software, Genome, Computational Biology, Databases, Genetic, Molecular Sequence Annotation

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