Abstract
The EnsMart system (www.ensembl.org/EnsMartGo) 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.
Users
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