title: Ensembl Genomes 2013: scaling up access to genome-wide data.
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.
authors.affiliation: The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK, Wellcome Trust Sanger Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK, Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA and USDA-ARS, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Paul Julian
authors.initials: PJ
authors.lastname: Kersey
authors.forename: James E
authors.initials: JE
authors.lastname: Allen
authors.forename: Mikkel
authors.initials: M
authors.lastname: Christensen
authors.forename: Paul
authors.initials: P
authors.lastname: Davis
authors.forename: Lee J
authors.initials: LJ
authors.lastname: Falin
authors.forename: Christoph
authors.initials: C
authors.lastname: Grabmueller
authors.forename: Daniel Seth Toney
authors.initials: DS
authors.lastname: Hughes
authors.forename: Jay
authors.initials: J
authors.lastname: Humphrey
authors.forename: Arnaud
authors.initials: A
authors.lastname: Kerhornou
authors.forename: Julia
authors.initials: J
authors.lastname: Khobova
authors.forename: Nicholas
authors.initials: N
authors.lastname: Langridge
authors.forename: Mark D
authors.initials: MD
authors.lastname: McDowall
authors.forename: Uma
authors.initials: U
authors.lastname: Maheswari
authors.forename: Gareth
authors.initials: G
authors.lastname: Maslen
authors.forename: Michael
authors.initials: M
authors.lastname: Nuhn
authors.forename: Chuang Kee
authors.initials: CK
authors.lastname: Ong
authors.forename: Michael
authors.initials: M
authors.lastname: Paulini
authors.forename: Helder
authors.initials: H
authors.lastname: Pedro
authors.forename: Iliana
authors.initials: I
authors.lastname: Toneva
authors.forename: Mary Ann
authors.initials: MA
authors.lastname: Tuli
authors.forename: Brandon
authors.initials: B
authors.lastname: Walts
authors.forename: Gareth
authors.initials: G
authors.lastname: Williams
authors.forename: Derek
authors.initials: D
authors.lastname: Wilson
authors.forename: Ken
authors.initials: K
authors.lastname: Youens-Clark
authors.forename: Marcela K
authors.initials: MK
authors.lastname: Monaco
authors.forename: Joshua
authors.initials: J
authors.lastname: Stein
authors.forename: Xuehong
authors.initials: X
authors.lastname: Wei
authors.forename: Doreen
authors.initials: D
authors.lastname: Ware
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Bolser
authors.forename: Kevin Lee
authors.initials: KL
authors.lastname: Howe
authors.forename: Eugene
authors.initials: E
authors.lastname: Kulesha
authors.forename: Daniel
authors.initials: D
authors.lastname: Lawson
authors.forename: Daniel Michael
authors.initials: DM
authors.lastname: Staines
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D002523:Edible Grain / Q000235:genetics; D016678:Genome; D016680:Genome, Bacterial; D016681:Genome, Fungal; D018745:Genome, Plant; D023281:Genomics; D020407:Internet; D058977:Molecular Sequence Annotation; D012984:Software