Biomedical Engineering Reference
In-Depth Information
into web pages. The GGA Ketcher [26] structure editor available in
ChemSpider was chosen as the structure editor of choice and implemented
in the structure drawing extension because it is easy to use and is based
on Javascript so does not require any extra additional add-ins or Flash
support to be installed (which could be a problem in a school environment).
It was also very easy to integrate into a MediaWiki extension. To
incorporate a Ketcher drawing frame into a HTML page, it was simply
necessary to download the Javascript and CSS fi les that comprise the
Ketcher code, reference these in the head section of the HTML of a wiki,
add the Ketcher frame, table and buttons to the body of the HTML, and
add an onload attribute to the page to initialize the Ketcher frame. The
only part of these steps which was not immediately straightforward for a
version 1.16.0 MediaWiki extension to add to the web page in which it
was called, was the step of adding an onload attribute to the page, but a
workaround was used that involved adding a Javascript function to the
HTML head, which was called at the window's onload event. The
resulting extension was called the KetcherDrawer extension.
The accompanying extension would add a Search button and would
need to perform several actions when clicked. The fi rst action is to take
the MOL depiction of the molecule that has been drawn (which is easily
retrieved via a call to the Ketcher Javascript functions) and convert it into
an InChI key so that this can be searched on. This conversion is done
using the IUPAC InChI code [59], and any warnings that are returned are
displayed in the wiki page, for example if stereochemistry is undefi ned or
any atom has an unusual valence. The next action is to post this InChIKey
to a search of the wiki - this was done by using the MediaWiki API to
silently retrieve the results of this search. If one matching substance page
was found then the page would redirect to view it. If no match for the full
InChIKey was found, then a second search was submitted to the
MediaWiki API to fi nd any matches for just the fi rst half of the InChIKey.
This roughly equates to broadening the search to fi nd matches for the
molecule's skeleton. Any results from this search are listed in the wiki
page itself, with a warning that no exact match could be found for the
molecule but that these are similar molecules. After these two extensions
had been written, it was then possible to add the functionality to perform
a structure search within the wiki just by calling the KetcherDrawer and
KetcherQuizAnswer extensions in the page.
A DisplaySpectrum extension was also written to add an interactive
spectrum to a wiki page. As explained earlier, we use two possible display
tools for spectra: JspecView and the ChemDoodle spectral display.
Approximately two-thirds of current viewers of the RSC educational web
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