Biomedical Engineering Reference
In-Depth Information
(described below). Each query was turned into a REST-ful web service
via an in-house framework known as BioServices. This acts a wrapper
around queries and takes care of many common functions such as load
balancing, authentication, output formatting and metadata descriptions.
Consequently, each query service ('QWS' in the fi gure) is a standardised,
parameterised endpoint that provides results in a variety of formats
including XML and JSON. A further advantage of this approach is that
these services (such as 'general information for a protein', 'ontology
mappings for a protein') are also available outside of Targetpedia.
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Data loading: a MediaWiki 'bot [24] was developed to carry out the
loading of data into Targetpedia. A 'bot is simply a piece of software
that can interact with the MediaWiki system to load large amounts of
content directly into the backend database. Each query service was
registered with the 'bot, along with a corresponding wiki template that
would hold the actual data. Templates [25] are similar to classes within
object-orientated programming in that they defi ne the fi elds (properties)
of a complex piece of data. Critically, templates also contain a
defi nition of how the data should be rendered in HTML (within the
wiki). This approach separates the data from the presentation, allowing
a fl exible interface design and multiple views across the same object.
With these two critical pieces in place, the 'bot was then able to access
the data and load it into the system via the MediaWiki API [26].
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Update scheduling: as different sources update content at different
rates, the system was designed such that administrators could refresh
different elements of the wiki under different schedules. Furthermore,
as one might often identify errors or omissions affecting only a subset
of entries, the loader was designed such that any update could be
limited to a list of specifi c proteins if desired. Thus, administrators
have complete control over which sources and entries can be updated
at any particular time.
The result of this process was a wiki populated with data covering the
major entity types in a semantically enriched format. Figure 17.2 shows
an excerpt of the types of properties and values stored for the protein,
phosphodiesterase 5.
17.1.3 The product and user experience
The starting point for most users is the protein information pages.
Figure 17.3 shows one such example.
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