Biomedical Engineering Reference
In-Depth Information
9
Creating an in-house 'omics data
portal using EBI Atlas software
Ketan Patel, Misha Kapushesky
and David Dean
Abstract:
The amount of public gene expression data has dramatically
increased in recent years. This has resulted in several efforts to
curate and make accessible this huge amount of public data in a
useful and easy to use way. One such project, the European
Bioinformatics Institute's Gene Expression Atlas, led to the
development of a portal that was intuitive to use and yet still
incorporated sophisticated queries and statistical analysis results.
The authors describe how the public Atlas project was adapted to
become a standalone product, which can be installed anywhere.
This Atlas allows both private companies and public institutes to
develop in-house data portals.
Key words:
gene expression; microarray; portal; 'omics; curation;
MAGE-TAB; intuitive user interface.
9.1 Introduction
Within the pharmaceutical industry, there is an ever increasing amount of
biological data being generated. Much of this data is from the 'omics
disciplines such as transcriptomics, proteomics and metabolomics. The
most prevalent of these is transcriptomics, with a mountain of public
data available and increasing amounts generated within companies. To
process, analyze and interpret this data requires sophisticated software,
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