Biomedical Engineering Reference
In-Depth Information
This chapter will fi rst outline a few basic tasks one can perform
with the Bioclipse-OpenTox platform, including the calculation of
molecular descriptors (which can also be used to calculate properties
important to toxicology, including logP and pK a ), the sharing of data on
toxins and toxicants online, and how Bioclipse supports authorization
and authentication on the OpenTox network. After that, two more
elaborate use cases will be presented, which will make use of the Decision
Support extension. Bioclipse Decision Support was developed by the
Department of Pharmaceutical Biosciences, Uppsala University, Sweden,
and AstraZeneca R&D, Mölndal, Sweden, with the goal of building an
extensible platform for integrating multiple predictive models with a
responsive user interface. Bioclipse Decision Support is now being used
for ADME-T predictions within AstraZeneca R&D.
2.2 Basic Bioclipse-OpenTox
interaction examples
As an introduction to the Bioclipse-OpenTox interoperability, this
chapter will fi rst introduce a few short examples. Of course, to reproduce
these examples yourself, you may have to familiarize yourself with the
Bioclipse software, which takes, like any other software, some time to
learn. However, the examples given in this chapter will not be that basic.
For more tutorials on how to use Bioclipse, we refer the reader to http://
www.opentox.org/tutorials/bioclipse .
Figure 2.1 shows the fi rst Bioclipse-OpenTox integration and highlights
the Bioclipse QSAR environment for calculating molecular properties
and theoretical descriptors [21]. This environment has been extended to
discover OpenTox services on the internet. Using this approach, Bioclipse
has access to the most recent descriptors relevant to toxicity predictions.
The fi gure shows the equivalence of a number of descriptors provided
by both local services (CDK and CDK REST, provided by the Chemistry
Development Kit library [22]) and OpenTox, as well as the Ionization
Potential descriptor provided only via an OpenTox computational
service. Practically, these online computational services are found by
querying a registry of OpenTox services: this registry makes use of the
OpenTox ontology [17], which Bioclipse queries, as outlined in [10]. The
ability to compute descriptors using various local and remote providers
creates a fl exible application for integration of numerical inputs for
statistical modeling of toxicologically relevant endpoints, as well as
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