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      Is Open Access

      Ensembl BioMarts: a hub for data retrieval across taxonomic space

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          Abstract

          For a number of years the BioMart data warehousing system has proven to be a valuable resource for scientists seeking a fast and versatile means of accessing the growing volume of genomic data provided by the Ensembl project. The launch of the Ensembl Genomes project in 2009 complemented the Ensembl project by utilizing the same visualization, interactive and programming tools to provide users with a means for accessing genome data from a further five domains: protists, bacteria, metazoa, plants and fungi. The Ensembl and Ensembl Genomes BioMarts provide a point of access to the high-quality gene annotation, variation data, functional and regulatory annotation and evolutionary relationships from genomes spanning the taxonomic space. This article aims to give a comprehensive overview of the Ensembl and Ensembl Genomes BioMarts as well as some useful examples and a description of current data content and future objectives.

          Database URLs: http://www.ensembl.org/biomart/martview/; http://metazoa.ensembl.org/biomart/martview/; http://plants.ensembl.org/biomart/martview/; http://protists.ensembl.org/biomart/martview/; http://fungi.ensembl.org/biomart/martview/; http://bacteria.ensembl.org/biomart/martview/

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          Most cited references21

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          Global variation in copy number in the human genome.

          Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.
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            Ensembl 2011

            The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.
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              The Ensembl automatic gene annotation system.

              As more genomes are sequenced, there is an increasing need for automated first-pass annotation which allows timely access to important genomic information. The Ensembl gene-building system enables fast automated annotation of eukaryotic genomes. It annotates genes based on evidence derived from known protein, cDNA, and EST sequences. The gene-building system rests on top of the core Ensembl (MySQL) database schema and Perl Application Programming Interface (API), and the data generated are accessible through the Ensembl genome browser (http://www.ensembl.org). To date, the Ensembl predicted gene sets are available for the A. gambiae, C. briggsae, zebrafish, mouse, rat, and human genomes and have been heavily relied upon in the publication of the human, mouse, rat, and A. gambiae genome sequence analysis. Here we describe in detail the gene-building system and the algorithms involved. All code and data are freely available from http://www.ensembl.org.
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                Author and article information

                Journal
                Database (Oxford)
                database
                databa
                Database: The Journal of Biological Databases and Curation
                Oxford University Press
                1758-0463
                2011
                23 July 2011
                23 July 2011
                : 2011
                : bar030
                Affiliations
                1European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and 2Department of Computer Science and Technology, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
                Author notes
                * Corresponding author. Rhoda J. Kinsella. Tel: +44 (0)1223 492608; Fax: +44 (0)1223 494484; Email: rhoda@ 123456ebi.ac.uk , helpdesk@ 123456ensembl.org
                Correspondence may also be addressed to Paul Flicek. Tel: +44 (0)1223 429581; Fax: +44 (0)1223 494484; Email: flicek@ 123456ebi.ac.uk

                Present address: Jorge Zamora, Structural Computational Biology Group, Spanish National Cancer Research Centre, C/ Melchor Fernández Almagro, 3, 28029, Madrid, Spain

                Article
                bar030
                10.1093/database/bar030
                3170168
                21785142
                f24cc355-73e1-4f27-80f4-a1160ddc40c7
                © The Author(s) 2011. Published by Oxford University Press.

                This is Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 20 April 2011
                : 12 June 2011
                : 16 June 2011
                Page count
                Pages: 9
                Categories
                Original Article

                Bioinformatics & Computational biology
                Bioinformatics & Computational biology

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