[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] ABSTRACT: Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (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. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data, and are participants in a growing range of collaborations involved in the annotation and analysis of genomes.
[Show abstract][Hide abstract] ABSTRACT: Ensembl Genomes (http://www.ensemblgenomes.org) is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed
using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria,
protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl.
Many of the databases supporting the portal have been built in close collaboration with the scientific community, which we
consider as essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which
include a graphical genome browser, FTP, BLAST search, a query optimised data warehouse, programmatic access, and a Perl API)
is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references
to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism
visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined
clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the