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Ensembl 2024

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Harrison, Peter W, Amode, M Ridwan, Austine-Orimoloye, Olanrewaju, Azov, Andrey G, Barba, Matthieu, Barnes, If, Becker, Arne, Bennett, Ruth +90 more·2024·Nucleic Acids Research
DOI 10.1093/nar/gkad1049PMC PMC10767893
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Abstract

Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.

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  • Gene location ground truth is annotated according to Ensembl Release 110, as collected in the MSigDB C1 gene set.

    “Ground truth is annotated according to Ensembl Release 110 [13], as collected in the MSigDB [29] C1 gene set (c1.all.v2023.2.Hs.symbols.gmt).”

    From LAB-Bench: Measuring Capabilities of Language Models for Biology Research (2024) · cites this paper as [13]

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Authors
Harrison, P. W., Amode, M. R., Austine-Orimoloye, O., Azov, A. G., Barba, M., Barnes, I., Becker, A., Bennett, R., Berry, A., Bhai, J., Bhurji, S. K., Boddu, S., Branco Lins, P. R., Brooks, L., Ramaraju, S. B., Campbell, L. I., Martinez, M. C., Charkhchi, M., Chougule, K., Cockburn, A., Davidson, C., De Silva, N. H., Dodiya, K., Donaldson, S., El Houdaigui, B., Naboulsi, T. E., Fatima, R., Giron, C. G., Genez, T., Grigoriadis, D., Ghattaoraya, G. S., Martinez, J. G., Gurbich, T. A., Hardy, M., Hollis, Z., Hourlier, T., Hunt, T., Kay, M., Kaykala, V., Le, T., Lemos, D., Lodha, D., Marques-Coelho, D., Maslen, G., Merino, G. A., Mirabueno, L. P., Mushtaq, A., Hossain, S. N., Ogeh, D. N., Sakthivel, M. P., Parker, A., Perry, M., Piližota, I., Poppleton, D., Prosovetskaia, I., Raj, S., Pérez-Silva, J. G., Salam, A. I. A., Saraf, S., Saraiva-Agostinho, N., Sheppard, D., Sinha, S., Sipos, B., Sitnik, V., Stark, W., Steed, E., Suner, M.-M., Surapaneni, L., Sutinen, K., Tricomi, F. F., Urbina-Gómez, D., Veidenberg, A., Walsh, T. A., Ware, D., Wass, E., Willhoft, N. L., Allen, J., Alvarez-Jarreta, J., Chakiachvili, M., Flint, B., Giorgetti, S., Haggerty, L., Ilsley, G. R., Keatley, J., Loveland, J. E., Moore, B., Mudge, J. M., Naamati, G., Tate, J., Trevanion, S. J., Winterbottom, A., Frankish, A., Hunt, S. E., Cunningham, F., Dyer, S., Finn, R. D., Martin, F. J., & Yates, A. D.
Affiliations
  • European Bioinformatics Institute (GB)
  • European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus , Hinxton , Cambridge , Cambridgeshire  CB10 1SD, UK
  • Cold Spring Harbor Laboratory (US)
  • Agricultural Research Service (US)
Corresponding author
Harrison, Peter W
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2023-11-11
Volume
52
Issue
D1
Pages
D891-D899
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkad1049
PMC
PMC10767893
OpenAlex
W4388615740
Cited by
742
References
3
Citations by year
2026: 220 · 2025: 385 · 2024: 134 · 2023: 2 · 2022: 1
FWCI
66.21
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
Funders
  • Wellcome Trust (222155/Z/20/Z, 226458/Z/22/Z, WT212925/Z/18/Z, 226083/Z/22/Z)
  • National Human Genome Research Institute of the National Institutes of Health (U24HG007234, U41HG010972, U24 HG002223,, R01HG010485, U24HG011451, U24HG007497)
  • National Institute of Allergy and Infectious Diseases of the National Institutes of Health (75N93019C00077)
  • The Biotechnology and Biological Sciences Research Council (BB/W019108/1, BB/T015608/1, BB/P016855/1, BB/S02011X/1, BB/T01461X/1, BB/W002965/1)
  • UK Medical Research Council (MR/S000453/1)
  • Open Targets
  • ELIXIR
  • European Molecular Biology Laboratory
  • European Union's Horizon 2020 (731060 (INFRAVEC2), 733161 (MultipleMS), 825575, 817923 (AQUA-FAANG), 817998 (GENE-SWitCH), 815668 (BovReg))
  • Horizon Europe programme (101059492, 101094718)
  • Gordon and Betty Moore Foundation (CBMF8897)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
Ensembl, genome annotation, reference genome, pan-genome, genome assembly annotation, comparative genomics, biodiversity genomics, Darwin Tree of Life, livestock, regulatory annotation, model organisms
MeSH terms
Animals, Humans, Phylogeny, Software, Genome, Genomics, Databases, Genetic, Molecular Sequence Annotation

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