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Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, Kersey P, Flicek P. Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford) 2011; 2011:bar030. [PMID: 21785142 PMCID: PMC3170168 DOI: 10.1093/database/bar030] [Citation(s) in RCA: 865] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/12/2011] [Accepted: 06/16/2011] [Indexed: 11/20/2022]
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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Affiliation(s)
- Rhoda J. Kinsella
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Department of Computer Science and Technology, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
| | - Andreas Kähäri
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Department of Computer Science and Technology, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
| | - Syed Haider
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Department of Computer Science and Technology, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
| | - Jorge Zamora
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Department of Computer Science and Technology, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
| | - Glenn Proctor
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Department of Computer Science and Technology, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
| | - Giulietta Spudich
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Department of Computer Science and Technology, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
| | - Jeff Almeida-King
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Department of Computer Science and Technology, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
| | - Daniel Staines
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Department of Computer Science and Technology, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
| | - Paul Derwent
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Department of Computer Science and Technology, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
| | - Arnaud Kerhornou
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Department of Computer Science and Technology, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
| | - Paul Kersey
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Department of Computer Science and Technology, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
| | - Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Department of Computer Science and Technology, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
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Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D. Gramene database in 2010: updates and extensions. Nucleic Acids Res 2010; 39:D1085-94. [PMID: 21076153 PMCID: PMC3013721 DOI: 10.1093/nar/gkq1148] [Citation(s) in RCA: 143] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene began with the addition of an Ensembl genome browser and has expanded in the last decade to become a robust resource for plant genomics hosting a wide array of data sets including quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps from various published studies (genetic, physical, bin, etc.). In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data.
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Affiliation(s)
- Ken Youens-Clark
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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Abe F, Amidei D, Apollinari G, Atac M, Auchincloss P, Baden A, Bailey M, Bamberger A, Barnett B, Barbaro-Galtieri A, Barnes V, Baumann T, Bedeschi F, Behrends S, Belforte S, Bellettini G, Bellinger J, Bensinger J, Beretvas A, Berge J, Bertolucci S, Bhadra S, Binkley M, Blair R, Blocker C, Bolognesi V, Booth A, Boswell C, Brandenburg G, Brown D, Buckley-Geer E, Budd H, Byon A, Byrum K, Campagnari C, Campbell M, Carey R, Carithers W, Carlsmith D, Carroll J, Cashmore R, Cervelli F, Chadwick K, Chiarelli G, Chinowsky W, Cihangir S, Clark A, Connor D, Contreras M, Cooper J, Cordelli M, Crane D, Curatolo M, Day C, Dell'Agnello S, Dell'Orso M, Demortier L, Derwent P, Devlin T, DiBitonto D, Drucker R, Elias J, Ely R, Eno S, Errede S, Esposito B, Flaugher B, Foster G, Franklin M, Freeman J, Frisch H, Fuess T, Fukui Y, Funayama Y, Garfinkel A, Gauthier A, Geer S, Giannetti P, Giokaris N, Giromini P, Gladney L, Gold M, Goulianos K, Grassmann H, Grosso-Pilcher C, Haber C, Hahn S, Handler R, Hara K, Harris R, Hauser J, Hawk C, Hessing T, Hollebeek R, Holloway L, Hu P, Hubbard B, Huffman B, Hughes R, Hurst P, Huth J, Incagli M, Ino T, Iso H, Jensen H, Jessop C, Johnson R, Joshi U, Kadel R, Kamon T, Kanda S, Kardelis D, Karliner I, Kearns E, Keeble L, Kephart R, Kesten P, Keup R, Keutelian H, Kim D, Kim S, Kirsch L, Kondo K, Konigsberg J, Kovacs E, Kuhlmann S, Kuns E, Laasanen A, Lamoureux J, Leone S, Li W, Liss T, Lockyer N, Luchini C, Maas P, Maeshima K, Mangano M, Marriner J, Markeloff R, Markosky L, Mattingly R, McIntyre P, Menzione A, Meyer T, Mikamo S, Miller M, Mimashi T, Miscetti S, Mishina M, Miyashita S, Morita Y, Moulding S, Mueller J, Mukherjee A, Nakae L, Nakano I, Nelson C, Newman-Holmes C, Ng J, Ninomiya M, Nodulman L, Ogawa S, Paoletti R, Para A, Pare E, Patrick J, Phillips T, Plunkett R, Pondrom L, Proudfoot J, Punzi G, Quarrie D, Ragan K, Redlinger G, Rhoades J, Roach M, Rimondi F, Ristori L, Rohaly T, Roodman A, Sakumoto W, Sansoni A, Sard R, Savoy-Navarro A, Scarpine V, Schlabach P, Schmidt E, Schub M, Schwitters R, Scribano A, Segler S, Seiya Y, Sekiguchi M, Shapiro M, Shaw N, Sheaff M, Shochet M, Siegrist J, Sinervo P, Skarha J, Sliwa K, Smith D, Snider F, Song L, St. Denis R, Stefanini A, Sullivan G, Swartz R, Takano M, Tartarelli F, Takikawa K, Tarem S, Theriot D, Timko M, Tipton P, Tkaczyk S, Tollestrup A, Tonnison J, Trischuk W, Tsay Y, Ukegawa F, Underwood D, Vejcik S, Vidal R, Wagner R, Wagner R, Wainer N, Walsh J, Watts T, Webb R, Wendt C, Wester W, Westhusing T, White S, Wicklund A, Williams H, Winer B, Yagil A, Yamashita A, Yasuoka K, Yeh G, Yoh J, Yokoyama M, Yun J, Zetti F. Measurement of the e+e- Invariant-Mass Distribution in p-barp Collisions at s=1.8 TeV. Phys Rev Lett 1991; 67:2418-2422. [PMID: 10044421 DOI: 10.1103/physrevlett.67.2418] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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