Biomedical Engineering Reference
In-Depth Information
example, the Novartis Institutes for BioMedical Research (NIBR [22])
conducts research aimed at drug discovery and development and is
developing an instance of selected ISA software components integrated as
part of an extended workfl ow for a microarray gene expression resource.
Janssen Research & Development, LLC (
http://www.janssenrnd.com
)
discovers and develops innovative medicines in several therapeutic areas
including immunology where the ISA framework is being used to collect,
annotate, and search relevant data sets. The use of these software
components is aimed at enhancing curation efforts for data integration
and analysis of in-house and public data sets. Furthermore, the endorsement
of the ISA software by public systems, continued community engagement
and growing list of project contributors have engendered a bioscience
'commons' of interoperable tools and data sets [21, 23]. The collaborative
ISA framework offers a novel approach to the unsettled status quo by
restricting itself to the harmonization of the structure of experimental
meta-data only, allowing users of (parts of) data sets to 'connect the meta-
data dots'. Harmonization of experimental meta-data is important for
many resource providers, as our case studies illustrate, for more effi cient
and better-informed comparison of studies across assays and domains.
To better understand the use of the ISA framework and related
developments, we offer the example of the curation process for the
European PredTox data sets - a collaborative, distributed study where
source material is subject to several kinds of assay in parallel in the search
for markers to predict the toxicity of drug candidates [24-27]. The ISA
framework was used to enable standards-compliant harmonization and
curation prior to the release of study to the public in 2011.
7.3.4 The InnoMed PredTox case study
PredTox [28] was part of the InnoMed Integrated Project, coordinated by
the European Federation of Pharmaceutical Industries and Associations
(EFPIA [29]), a body representing the research-based pharmaceutical
industries and biotech SMEs operating in Europe. InnoMed is a precursor
to the Innovative Medicines Initiative, IMI; Europe's largest current
public-private initiative [30] with 19 partners (14 pharma companies,
three universities, two technology providers). The goal of PredTox was to
assess the value of combining results from 'omics technologies with the
results from more conventional toxicology methods to support more
informed decision-making in pre-clinical safety evaluation. An overview
of the PredTox data sets is given in Figure 7.2. The depth and breadth of
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