Genome Research

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

Genome Res. 14:160-169, 2004
©2004 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/04 $5.00
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Kasprzyk, A.
Right arrow Articles by Birney, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Kasprzyk, A.
Right arrow Articles by Birney, E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Resources

EnsMart: A Generic System for Fast and Flexible Access to Biological Data

Arek Kasprzyk1,3, Damian Keefe1, Damian Smedley1, Darin London1, William Spooner2, Craig Melsopp1, Martin Hammond1, Philippe Rocca-Serra1, Tony Cox2 and Ewan Birney1

1 European Bioinformatics Institute (EBI), Hinxton, Cambridge CB10 1SH, UK 2 The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SH, UK

The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools. The system consists of a query-optimized database and interactive, user-friendly interfaces. EnsMart has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval of customized data sets. A wide variety of complex queries, on various types of annotations, for numerous species are supported. These can be applied to many research problems, ranging from SNP selection for candidate gene screening, through cross-species evolutionary comparisons, to microarray annotation. Users can group and refine biological data according to many criteria, including cross-species analyses, disease links, sequence variations, and expression patterns. Both tabulated list data and biological sequence output can be generated dynamically, in HTML, text, Microsoft Excel, and compressed formats. A wide range of sequence types, such as cDNA, peptides, coding regions, UTRs, and exons, with additional upstream and downstream regions, can be retrieved. The EnsMart database can be accessed via a public Web site, or through a Java application suite. Both implementations and the database are freely available for local installation, and can be extended or adapted to `non-Ensembl' data sets.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1645104.

3 Corresponding author.
E-MAIL arek{at}ebi.ac.uk; FAX 44-1223-494468.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Genome Res.Home page
I. Hellmann, Y. Mang, Z. Gu, P. Li, F. M. de la Vega, A. G. Clark, and R. Nielsen
Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
Genome Res., July 1, 2008; 18(7): 1020 - 1029.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
F. Lemoine, B. Labedan, and C. Froidevaux
GenoQuery: a new querying module for functional annotation in a genomic warehouse
Bioinformatics, July 1, 2008; 24(13): i322 - i329.
[Abstract] [PDF]

Home page
 Nucleic Acids ResHome page
D. Aguilar, L. Skrabanek, S. S. Gross, B. Oliva, and F. Campagne
Beyond tissueInfo: functional prediction using tissue expression profile similarity searches
Nucleic Acids Res., June 1, 2008; 36(11): 3728 - 3737.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
D. Ge, K. Zhang, A. C. Need, O. Martin, J. Fellay, T. J. Urban, A. Telenti, and D. B. Goldstein
WGAViewer: Software for genomic annotation of whole genome association studies
Genome Res., April 1, 2008; 18(4): 640 - 643.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
Z. Du, Y. Zhao, and N. Li
Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription
Genome Res., February 1, 2008; 18(2): 233 - 241.
[Abstract] [Full Text] [PDF]

Home page
 Toxicol SciHome page
K. Nohara, K. Ao, Y. Miyamoto, T. Suzuki, S. Imaizumi, Y. Tateishi, S. Omura, C. Tohyama, and T. Kobayashi
Arsenite-Induced Thymus Atrophy is Mediated by Cell Cycle Arrest: A Characteristic Downregulation of E2F-Related Genes Revealed by a Microarray Approach
Toxicol. Sci., February 1, 2008; 101(2): 226 - 238.
[Abstract] [Full Text] [PDF]

Home page
 Brief Funct Genomic ProteomicHome page
J. M. Hancock and A.-M. Mallon
Phenobabelomics mouse phenotype data resources
Brief Funct Genomic Proteomic, January 11, 2008; (2008) elm033v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. A. Bruford, M. J. Lush, M. W. Wright, T. P. Sneddon, S. Povey, and E. Birney
The HGNC Database in 2008: a resource for the human genome
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D445 - D448.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Flicek, B. L. Aken, K. Beal, B. Ballester, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, et al.
Ensembl 2008
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D707 - D714.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. G. Wilming, J. G. R. Gilbert, K. Howe, S. Trevanion, T. Hubbard, and J. L. Harrow
The vertebrate genome annotation (Vega) database
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D753 - D760.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Birzele, R. Kuffner, F. Meier, F. Oefinger, C. Potthast, and R. Zimmer
ProSAS: a database for analyzing alternative splicing in the context of protein structures
Nucleic Acids Res., January 1, 2008; 36(suppl_1): D63 - D68.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
T. Derrien, C. Andre, F. Galibert, and C. Hitte
Analysis of the Unassembled Part of the Dog Genome Sequence: Chromosomal Localization of 115 Genes Inferred from Multispecies Comparative Genomics
J. Hered., August 3, 2007; (2007) esm027v3.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Labarga, F. Valentin, M. Anderson, and R. Lopez
Web Services at the European Bioinformatics Institute
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W6 - W11.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Reimand, M. Kull, H. Peterson, J. Hansen, and J. Vilo
g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W193 - W200.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
J. Adachi, C. Kumar, Y. Zhang, and M. Mann
In-depth Analysis of the Adipocyte Proteome by Mass Spectrometry and Bioinformatics
Mol. Cell. Proteomics, July 1, 2007; 6(7): 1257 - 1273.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. Taylor, W. Valdar, A. Kumar, J. Flint, and R. Mott
Management, presentation and interpretation of genome scans using GSCANDB
Bioinformatics, June 15, 2007; 23(12): 1545 - 1549.
[Abstract] [Full Text] [PDF]

Home page
 Toxicol SciHome page
Y. Guo, R. A. Jolly, B. W. Halstead, T. K. Baker, J. P. Stutz, M. Huffman, J. N. Calley, A. West, H. Gao, G. H. Searfoss, et al.
Underlying Mechanisms of Pharmacology and Toxicity of a Novel PPAR Agonist Revealed Using Rodent and Canine Hepatocytes
Toxicol. Sci., April 1, 2007; 96(2): 294 - 309.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
X. Gu
Evolutionary Framework for Protein Sequence Evolution and Gene Pleiotropy
Genetics, April 1, 2007; 175(4): 1813 - 1822.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. G. Gilbert
DroSpeGe: rapid access database for new Drosophila species genomes
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D480 - D485.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. E. Higgins, M. Claremont, J. E. Major, C. Sander, and A. E. Lash
CancerGenes: a gene selection resource for cancer genome projects
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D721 - D726.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
O. Arnaiz, S. Cain, J. Cohen, and L. Sperling
ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D439 - D444.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Gattiker, C. Niederhauser-Wiederkehr, J. Moore, L. Hermida, and M. Primig
The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D457 - D462.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Lawson, P. Arensburger, P. Atkinson, N. J. Besansky, R. V. Bruggner, R. Butler, K. S. Campbell, G. K. Christophides, S. Christley, E. Dialynas, et al.
VectorBase: a home for invertebrate vectors of human pathogens
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D503 - D505.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. J. P. Hubbard, B. L. Aken, K. Beal, B. Ballester, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, et al.
Ensembl 2007
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D610 - D617.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. N. Twigger, M. Shimoyama, S. Bromberg, A. E. Kwitek, H. J. Jacob, and the RGD Team
The Rat Genome Database, update 2007--Easing the path from disease to data and back again
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D658 - D662.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. Chaurasia, Y. Iqbal, C. Hanig, H. Herzel, E. E. Wanker, and M. E. Futschik
UniHI: an entry gate to the human protein interactome
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D590 - D594.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. M. Hulbert, L. J. Smink, E. C. Adlem, J. E. Allen, D. B. Burdick, O. S. Burren, C. C. Cavnor, G. E. Dolman, D. Flamez, K. F. Friery, et al.
T1DBase: integration and presentation of complex data for type 1 diabetes research
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D742 - D746.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
B.-Y. Liao, N. M. Scott, and J. Zhang
Impacts of Gene Essentiality, Expression Pattern, and Gene Compactness on the Evolutionary Rate of Mammalian Proteins
Mol. Biol. Evol., November 1, 2006; 23(11): 2072 - 2080.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
J. E. Stajich and H. Lapp
Open source tools and toolkits for bioinformatics: significance, and where are we?
Brief Bioinform, September 1, 2006; 7(3): 287 - 296.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
B.-Y. Liao and J. Zhang
Low Rates of Expression Profile Divergence in Highly Expressed Genes and Tissue-Specific Genes During Mammalian Evolution
Mol. Biol. Evol., June 1, 2006; 23(6): 1119 - 1128.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Blake, C. Schwager, M. Kapushesky, and A. Brazma
ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression
Bioinformatics, March 15, 2006; 22(6): 765 - 767.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
B.-Y. Liao and J. Zhang
Evolutionary Conservation of Expression Profiles Between Human and Mouse Orthologous Genes
Mol. Biol. Evol., March 1, 2006; 23(3): 530 - 540.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
Z. Su, J. Wang, J. Yu, X. Huang, and X. Gu
Evolution of alternative splicing after gene duplication
Genome Res., February 1, 2006; 16(2): 182 - 189.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Holste, G. Huo, V. Tung, and C. B. Burge
HOLLYWOOD: a comparative relational database of alternative splicing
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D56 - D62.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. M. Schwarz, I. Antoshechkin, C. Bastiani, T. Bieri, D. Blasiar, P. Canaran, J. Chan, N. Chen, W. J. Chen, P. Davis, et al.
WormBase: better software, richer content
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D475 - D478.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. Birney, D. Andrews, M. Caccamo, Y. Chen, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, et al.
Ensembl 2006
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D556 - D561.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
L. Verlinden, G. Eelen, I. Beullens, M. Van Camp, P. Van Hummelen, K. Engelen, R. Van Hellemont, K. Marchal, B. De Moor, F. Foijer, et al.
Characterization of the Condensin Component Cnap1 and Protein Kinase Melk as Novel E2F Target Genes Down-regulated by 1,25-Dihydroxyvitamin D3
J. Biol. Chem., November 11, 2005; 280(45): 37319 - 37330.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Wang, P. J. Smith, A. R. Krainer, and M. Q. Zhang
Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes
Nucleic Acids Res., September 7, 2005; 33(16): 5053 - 5062.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Durinck, Y. Moreau, A. Kasprzyk, S. Davis, B. De Moor, A. Brazma, and W. Huber
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
Bioinformatics, August 15, 2005; 21(16): 3439 - 3440.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Roepcke, P. Fiziev, P. H. Seeburg, and M. Vingron
SVC: structured visualization of evolutionary sequence conservation
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W271 - W273.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
B. Zhang, S. Kirov, and J. Snoddy
WebGestalt: an integrated system for exploring gene sets in various biological contexts
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W741 - W748.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
S. Kamalakaran, S. K. Radhakrishnan, and W. T. Beck
Identification of Estrogen-responsive Genes Using a Genome-wide Analysis of Promoter Elements for Transcription Factor Binding Sites
J. Biol. Chem., June 3, 2005; 280(22): 21491 - 21497.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
S. E. Owens, K. W. Broman, T. Wiltshire, J. B. Elmore, K. M. Bradley, J. R. Smith, and E. M. Southard-Smith
Genome-wide linkage identifies novel modifier loci of aganglionosis in the Sox10Dom model of Hirschsprung disease
Hum. Mol. Genet., June 1, 2005; 14(11): 1549 - 1558.
[Abstract] [Full Text] [PDF]

Home page
 Genes Dev.Home page
P. Y. Chen, H. Manninga, K. Slanchev, M. Chien, J. J. Russo, J. Ju, R. Sheridan, B. John, D. S. Marks, D. Gaidatzis, et al.
The developmental miRNA profiles of zebrafish as determined by small RNA cloning
Genes & Dev., June 1, 2005; 19(11): 1288 - 1293.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
W.J. Kent, F. Hsu, D. Karolchik, R. M. Kuhn, H. Clawson, H. Trumbower, and D. Haussler
Exploring relationships and mining data with the UCSC Gene Sorter
Genome Res., May 1, 2005; 15(5): 737 - 741.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
U. Sarkans, H. Parkinson, G. G. Lara, A. Oezcimen, A. Sharma, N. Abeygunawardena, S. Contrino, E. Holloway, P. Rocca-Serra, G. Mukherjee, et al.
The ArrayExpress gene expression database: a software engineering and implementation perspective
Bioinformatics, April 15, 2005; 21(8): 1495 - 1501.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Tao, C. Friedman, and Y. A. Lussier
Visualizing information across multidimensional post-genomic structured and textual databases
Bioinformatics, April 15, 2005; 21(8): 1659 - 1667.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Brooksbank, G. Cameron, and J. Thornton
The European Bioinformatics Institute's data resources: towards systems biology
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D46 - D53.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Kersey, L. Bower, L. Morris, A. Horne, R. Petryszak, C. Kanz, A. Kanapin, U. Das, K. Michoud, I. Phan, et al.
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D297 - D302.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Chen, T. W. Harris, I. Antoshechkin, C. Bastiani, T. Bieri, D. Blasiar, K. Bradnam, P. Canaran, J. Chan, C.-K. Chen, et al.
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D383 - D389.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. Veeramachaneni and W. Makalowski
DED: Database of Evolutionary Distances
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D442 - D446.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Hubbard, D. Andrews, M. Caccamo, G. Cameron, Y. Chen, M. Clamp, L. Clarke, G. Coates, T. Cox, F. Cunningham, et al.
Ensembl 2005
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D447 - D453.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. L. Ashurst, C.-K. Chen, J. G. R. Gilbert, K. Jekosch, S. Keenan, P. Meidl, S. M. Searle, J. Stalker, R. Storey, S. Trevanion, et al.
The Vertebrate Genome Annotation (Vega) database
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D459 - D465.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. Elnitski, B. Giardine, P. Shah, Y. Zhang, C. Riemer, M. Weirauch, R. Burhans, W. Miller, and R. C. Hardison
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D466 - D470.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. Parkinson, U. Sarkans, M. Shojatalab, N. Abeygunawardena, S. Contrino, R. Coulson, A. Farne, G. Garcia Lara, E. Holloway, M. Kapushesky, et al.
ArrayExpress--a public repository for microarray gene expression data at the EBI
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D553 - D555.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
A. Baross, Y. S.N. Butterfield, S. M. Coughlin, T. Zeng, M. Griffith, O. L. Griffith, A. S. Petrescu, D. E. Smailus, J. Khattra, H. L. McDonald, et al.
Systematic Recovery and Analysis of Full-ORF Human cDNA Clones
Genome Res., October 1, 2004; 14(10b): 2083 - 2092.
[Abstract] [Full Text] [PDF]