Accessing Open PHACTS: interactive exploration of compounds and targets from the semantic web
Katrin Stierand
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2
Tim Harder
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2
Lothar Wissler
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1
Christian Lemmen
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1
Matthias Rarey
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2
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References 1. Gray AJG, Groth P, Loizou A, et al: Applying linked data approaches to pharmacology: Architectural decisions and implementation. Semantic Web 2012. 2. Azzaoui K, Jacoby E, Senger S, et al: Scientific competency questions as the basis for semantically enriched open pharmacological space development. Drug Discovery Today 2013. 3. Stierand K, Harder T, Marek T, et al: The Internet as Scientific Knowledge Base: Navigating the Chem-Bio Space. Mol Inf 2012
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31:543-546
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http:// www.chembionavigator.org. Describes an early version of CBN.
1
BioSolveIT GmbH
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An der Ziegelei 79, 53757 Sankt Augustin
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Germany
2
Center for Bioinformatics (ZBH), University of Hamburg
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Bundesstr. 43, 20146 Hamburg
,
Germany
2014 Stierand et al; licensee Chemistry Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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Pharmacological research is hampered by scattered data
which have to be retrieved by varying methods and in
different data formats. This heterogeneity increases
research costs and limits throughput. Over the last two
years, the Open PHACTS Discovery Platform [1] has
been developed as a centralized repository, integrating
pharmacological data from a variety of information
resources and providing tools and services to query
these integrated data in pharmacological research.
Following an application-oriented approach, the Open
PHACTS project started with the definition of potential
use cases in the form of prioritized research questions [2],
most of which can only be answered by accessing multiple
data sources in the web. The development of the platform
as well as the services has been guided by these questions.
Here, we present the ChemBioNavigator (CBN) [3], a
web application allowing to navigate the Open PHACTS
chem-bio space with a focus on small molecules and their
targets. CBN comprises of a large visualization area with
different view modes and two information panels, allowing
a deeper insight in information for compounds and
targets. It allows interactive exploration of compound sets
through sorting and subset selection as well as extending
sets by substructure or similarity search. The relation
between compounds and targets is defined by assay data
from the Discovery Platform. Each compound and each
target is annotated with information from multiple data
sources which is provided together with the provenance
for each data point.
In this contribution we roughly outline the
OpenPHACTS/CBN technology and present a number of
high-priority research questions, highlight the advantages
of exploiting the integrated data through the CBNs
smart and intuitive interface.
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