Biomedical Engineering Reference
In-Depth Information
information on the internet describing the MediaWiki API [55], and
examples of bot scripts to get started [56]. In two chapters in this topic,
Alquier (Chapter 16) and also Harland and co-workers (Chapter 17)
describe the benefi ts and application of semantic MediaWiki. For each
batch of substance pages to be created, an input fi le was made containing
the basic inputs required to populate the page. The bot script fi rstly
retrieves the login page of the wiki and supplies it with user credentials,
then logs in and retrieves a token to be used when accessing other pages
on the wiki. The script then recurses through the input fi le, constructs a
URL for each new substance page in edit mode, posts the new content,
and then saves the changes made. The Snoopy open source PHP class
[57] played the crucial role of effectively simulating a web browser in this
process - it was very well documented and straightforward to implement.
Discoverability is also important for these substance pages. An
important objective was to make the substance pages searchable by
structure (as ChemSpider is). An easy way to do this from outside the site
is to use the 'Add HTML Meta And Title' extension [58], which was used
to set the meta-data keywords and description on each substance page
for search engines to use, and making sure that the InChI key was
included in the meta-data. Structure searching within the wiki (not just
from internet search engines) is also necessary, so that students or teachers
can draw a molecule using a chemical drawing package embedded within
a wiki page. When they click on a Search button in the page, the InChI
key of the drawn structure is compared with that of all the substance
pages in the wiki, and any matches are returned. This is rather a specialized
requirement and required the development of a new extension. Developing
a new extension was made easier by investigating the range of extensions
that are already available for MediaWiki and reviewing the code behind
them which is enabled by the fact that the MediaWiki hooks and handlers
are all open source, well documented, and transparent. The functionality
of this structure search was split so as to create two new MediaWiki
extensions rather than one: the fi rst embedded a structure drawer into a
wiki page and the second added a Search button, which when clicked
would display the search results. The reason for splitting the functionality
into two separate extensions was that various other applications of the
structure drawer had been suggested (which will be described shortly)
and by this design the fi rst extension could be used for various other
applications without duplicating code.
Although a new MediaWiki extension needed to be developed to add a
structure editor to a wiki page, it was not necessary to start from scratch
as various open source structure editors already exist that can be embedded
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