RT Journal
A1 Kasprzyk, Arek
A1 Keefe, Damian
A1 Smedley, Damian
A1 London, Darin
A1 Spooner, William
A1 Melsopp, Craig
A1 Hammond, Martin
A1 Rocca-Serra, Philippe
A1 Cox, Tony
A1 Birney, Ewan
T1 EnsMart: A Generic System for Fast and Flexible Access to Biological Data
JF Genome Research 
JO Genome Research 
YR 2004 
FD January 01 
VO 14 
IS 1 
SP 160 
OP 169 
DO 10.1101/gr.1645104 
UL http://genome.cshlp.org/content/14/1/160.abstract 
AB 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.