Biomedical Engineering Reference
In-Depth Information
which is available both as open source packages and also several vendor
solutions. To date, most of the work in developing software has focused
on processing, analytics and storage of the data. This software has a high
learning curve and is not easily accessible without training. Within the
environment of a large pharmaceutical company, we saw a need to create
a portal where users could browse and query 'omics data sets, in an easy
to use way using just a web browser. This would enable a whole new
category of users to access the data and make sense of it, and hopefully
use it in day-to-day scientifi c decision making. The solution should also
complement existing 'omics infrastructure rather than replace it. Here,
we describe how we have adapted the European Bioinformatics Institute
(EBI) Gene Expression Atlas software (the Atlas), which was developed
for a similar purpose, into a standalone product that can be deployed
within a company fi rewall. This in-house installation of the Atlas allows
loading of public and internal data sets, and gives scientists access to
these data sets in a nice easy-to-use interface. First, we give an overview
of how 'omics data is used in the drug industry today, and the motivation
for building a portal. Next, we detail the process of adapting Atlas from
an existing public web site into an installable standalone piece of software.
Finally, an overview of deploying and running the portal within a large
company will be described.
9.2 Leveraging 'omics data for
drug discovery
9.2.1 'omics data is used throughout the drug
discovery and development pipeline
The use of 'omics data within drug discovery has increased in
recent years in particular gene expression profi ling using transcriptomics
[1]. In the past it was used in pre-clinical studies to understand
drug action, animal models of disease and also to understand toxicology.
Later, 'omics studies utilizing human samples became more prevalent,
and this is now done in all phases of the drug discovery and development
pipeline (see Figure 9.1). In the early phase of discovery, a typical scenario
is to look for differences in expression between normal and diseased
tissue (both in humans and in animals), to discover new potential
targets for therapeutic intervention [2]. It is also common at this
early stage to look at gene expression following compound treatment in
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