Ensembl Genomes 2013: scaling up access to genome-wide data

Kersey, P. J., Allen, J. E., Christensen, M., Davis, P., Falin, L. J., Grabmueller, C., Hughes, D. S., 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. (January 2014) Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Research, 42 (Databa). D546-52. ISSN 0305-1048

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URL: http://www.ncbi.nlm.nih.gov/pubmed/24163254
DOI: 10.1093/nar/gkt979

Abstract

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.

Item Type: Paper
Uncontrolled Keywords: Animals Cereals/genetics *Databases, Genetic *Genome Genome, Bacterial Genome, Fungal Genome, Plant Genomics Internet Molecular Sequence Annotation Software
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics > databases > databases
bioinformatics > genomics and proteomics > datasets
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:
Communities: CSHL labs > Ware lab
Depositing User: Matt Covey
Date: January 2014
Date Deposited: 11 Apr 2014 18:36
Last Modified: 11 Apr 2014 18:36
PMCID: PMC3965094
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29748

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