Biomedical Engineering Reference
In-Depth Information
modern standards compliant browsers that support HTML5 (for example
Google Chrome and Firefox) and, as described earlier, limits its use in
most versions of Internet Explorer unless the Google Chrome Frame
plug-in is installed. This form of spectral display has not yet been
implemented in the ChemSpider web interface but has been installed to
support the SpectralGame [39] [40] on mobile devices.
Although ChemSpider is not an open source project per se, depending
for its delivery on a Microsoft ASP.NET platform and SQL Server
database, it should be clear that the project does take advantage of many
open source components to deliver much of the functionality including
fi le format conversion and visualization. In particular the InChI identifi er,
a fully open source project, has been a pivotal technology in the
foundation of ChemSpider and has become essential in linking
the platform out to other databases on the internet using InChIs.
3.4 ChemDraw Digester
The ChemDraw Digester is an informatics project bridging the
previous two topics discussed - it is a tool that uses the structure
manipulation programs contained in ChemSpider's code to help enhance
RSC articles. In the fi rst section we saw that if the most important
chemical compounds in a paper can be identifi ed and deposited to
ChemSpider then the article can be enhanced with links to provide
readers with more compound information. These compounds were
generated by using name to structure algorithms after extraction of the
chemical identifi er. However, more often than defi ning a compound
by name, chemistry authors refer to and defi ne compounds in their
paper by fi gures in the manuscript where the molecular structures are
being discussed (see Figure 3.3) [41].
Where the images accompanying a manuscript have been generated
using the structure drawing package ChemDraw [42], the RSC requests
that authors supply these images not only as image fi les, but also in their
original ChemDraw format (with the fi le extension '.cdx'), as these fi les
preserve the chemical information of the structures within them. As the
ChemDraw fi le format can also incorporate graphical objects and text,
the fi les often contain labels (reference numbers or text) that correspond
to the references of the compound in the corresponding manuscript, as in
the example fi gure. Therefore, by 'digesting' a ChemDraw fi le we could
potentially decorate these occurrences of the compounds' identifying
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