The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Ensembl Genomes 2013: scaling up access to genome-wide data
Open accessAbstract
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.
Overview
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
Verification
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.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
Atwell, S., Huang, Y. S., Vilhjálmsson, B. J., Willems, G., Horton, M., Li, Y., Meng, D., Platt, A., Tarone, A. M., Hu, T. T., et al. (2010) · Nature · doi:10.1038/nature08800 · Cited by 1,780
A physical, genetic and functional sequence assembly of the barley genome
The International Barley Genome Sequencing Consortium (2012) · Nature · doi:10.1038/nature11543 · Cited by 1,456
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
Vilella, A. J., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R., & Birney, E. (2009) · Genome Research · doi:10.1101/gr.073585.107 · Cited by 1,238
PomBase: a comprehensive online resource for fission yeast
Wood, V., Harris, M. A., McDowall, M. D., Rutherford, K., Vaughan, B. W., Staines, D. M., Aslett, M., Lock, A., Bahler, J., Kersey, P. J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr853 · Cited by 321
Self-citation
Cited by
The Ensembl Variant Effect Predictor
McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R. S., Thormann, A., Flicek, P., & Cunningham, F. (2016) · Genome Biology · doi:10.1186/s13059-016-0974-4 · Cited by 8,099
Huerta-Cepas, J., Szklarczyk, D., Forslund, K., Cook, H., Heller, D., Walter, M. C., Rattei, T., Mende, D. R., Sunagawa, S., Kuhn, M., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1248 · Cited by 2,101
Cunningham, F., Amode, M. R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1010 · Cited by 1,115
Rfam 12.0: updates to the RNA families database
Nawrocki, E. P., Burge, S. W., Bateman, A., Daub, J., Eberhardt, R. Y., Eddy, S. R., Floden, E. W., Gardner, P. P., Jones, T. A., Tate, J., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1063 · Cited by 1,071
Berthelot, C., Brunet, F., Chalopin, D., Juanchich, A., Bernard, M., Noël, B., Bento, P., Da Silva, C., Labadie, K., Alberti, A., et al. (2014) · Nature Communications · doi:10.1038/ncomms4657 · Cited by 959
Metadata
- Authors
- Kersey, P. J., Allen, J. E., Christensen, M., Davis, P., Falin, L. J., Grabmueller, C., Hughes, D. S. T., Humphrey, J., Kerhornou, A., Khobova, J., Langridge, N., McDowall, M. D., Maheswari, U., Maslen, G., Nuhn, M., Ong, C. K., Paulini, M., Pedro, H., Toneva, I., Tuli, M. A., Walts, B., Williams, G., Wilson, D., Youens-Clark, K., Monaco, M. K., Stein, J., Wei, X., Ware, D., Bolser, D. M., Howe, K. L., Kulesha, E., Lawson, D., & Staines, D. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-10-25
- Volume
- 42
- Issue
- D1
- Pages
- D546-D552
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W1998808728
- Cited by
- 213
- References
- 5
- FWCI
- 16.54
- Type
- journal article
- Language
- en
- Open access
- gold
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Ensembl Genomes 2013: scaling up access to genome-wide data. https://app.cochat.ai/papers/10.1093/nar/gkt979
- The paper
- Kersey, P. J., Allen, J. E., Christensen, M., Davis, P., Falin, L. J., Grabmueller, C., Hughes, D. S. T., Humphrey, J., Kerhornou, A., Khobova, J., Langridge, N., McDowall, M. D., Maheswari, U., Maslen, G., Nuhn, M., Ong, C. K., Paulini, M., Pedro, H., Toneva, I., . . . Staines, D. M. (2014). Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Research. https://doi.org/10.1093/nar/gkt979
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
