Biomedical Engineering Reference
In-Depth Information
allow the source code to be modifi ed outside of their organization. This
platform was chosen over other possible solutions for ChemSpider as the
team was knowledgeable, professional and agile. The original version of
Bingo was made available only on SQL Server 2008 while ChemSpider
was running on SQL Server 2005 at that time. As the software was
available as open source, we recompiled the source code to work on SQL
Server 2005 and the GGA team fi xed version discrepancies quickly and
provided a working version of Bingo for SQL Server 2005 within a one-
day turnaround. This is a testament to the skills of the software team
supporting this open source product.
In order to perform both structure searching and substructure
searching, a manner by which to introduce a chemical structure drawing
is required. We provide access to a number of structure drawing tools,
both Java and JavaScript. Two of these structure editors are open source
(GGA's Ketcher [26] and JChemPaint [27]) and we implemented them
without modifi cation.
There are various needs on the ChemSpider system for the conversion
of chemical fi le formats and we utilize the open source OpenBabel
package for this purpose [28]. Although the software code was functional,
we have identifi ed a number of general issues with the code including
inversion of stereo centers and loss of other chemical information. We
believe that OpenBabel is a signifi cant contribution to the cheminformatics
community that will continue to improve in quality.
We generate 3D conformers on the fl y from the 2D layouts in the
database. We chose the freely available Balloon optimizer [29], primarily
because it is free and fast; and it is a command line tool and was relatively
easy to integrate. Balloon is not, however, open source, and cannot be
modifi ed. We use Jmol [30] to visualize the resulting optimized 3D
molecular structures as well as crystallographic fi les (CIFs) where
available. We do not use the Java-based JMol to visualize regular 2D
images as it can add a signifi cant load to browsers.
Literature linking from ChemSpider to open internet services has been
established in an automated fashion taking advantage of freely available
application programming interfaces to such web sites as PubMed [31],
Google Scholar [32] and Google Patents [33]. Validated chemical names
are used as the basis of a search against the PubMed database searching
only
against the title and the abstract. In this way, a search on cholesterol,
for example, would only retrieve those articles with cholesterol in the
title and abstract rather than the many tens of thousands of articles likely
to mention cholesterol in the body of the article. A similar approach has
been taken to integrate to Google Scholar and Google Patents. It should
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