Biomedical Engineering Reference
In-Depth Information
and from there navigate back to the project main page or any parent or
child assertion pages using the semantic network hyperlinks. In this
way the workbench is not only useful as a way to capture disease
knowledge but also provides a platform to present learning on diseases
and pathways to project teams across the company. As individual targets
and diseases are semantically indexed on the pages, one can explore
the knowledge base in many ways and move freely from one project
to another.
In summary, we have developed a knowledge system that allows
scientists to collaboratively build and share disease knowledge and
interpretation with a low barrier to adoption. Much of the data capture
process is deliberately manual - aiming to capture what the scientist thinks,
rather than what a database knows. However, future iterations of the tool
could benefi t from more intelligent and effi cient forms of data entry,
annotation and discovery. Better connectivity to internal databases would
be a key next step - as assertions are entered, they could be scanned and
connected to important results in corporate systems. Automatic semantic
tagging would be another area for improvement, the system recognising
entities as the text is typed and presenting the list of 'discovered' concepts
to the user who simply checks it is correct. Finally, we envisage a connection
with tools such as Utopia (see Chapter 15 by Pettifer and colleagues), that
would allow scientists to augment their assertions by sending quotes and
comments on scientifi c papers directly from the PDF reader to the wiki.
17.2.4 Lessons learned
The prototype disease knowledge workbench brings a new capability to
our biologists, enabling the capture of their understanding and
interpretation of disease mechanisms. However, there are defi nitely areas
for improvement. In particular, although the solution was based around
the writing of report-style content, the MediaWiki software lacks a
robust, intuitive interface for general editing. The FCKEditor component
provides some basic functionality, but it still feels as if it is not fully
integrated and lacks many common features. Incorporation of images
and other fi les needs to evolve to a 'drag and drop' method, rather than
the convoluted, multistep process used currently. Although we are aware
of the Semantic MediaWiki Plus extensions in these areas [39], in our
hands they were not intuitive to use and added too much complexity to
the interface. Thus, the development of components to make editing
content much more user-friendly should be a high priority and one that,
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