Biomedical Engineering Reference
In-Depth Information
By themselves, these objects are 'inert', but they come alive when
semantically tied to assertions. For instance, for the hypothesis 'Altered
monocyte cytokine release contributes to immunosuppression in sepsis',
one can attach the entities involved such as monocyte cells and specifi c
cytokine proteins. This 'semantic tagging' builds up comprehensive
relationships between pathophysiology and the cellular and molecular
components that underlie these effects. They also enable the identifi cation
of shared biology. For instance, the wiki can store all known molecular
pathways as observations; assigning all of the protein members to it via
semantic tagging. Then, as authors of other assertions tag their pages
with the principle proteins involved, an ASK query can automatically
identify relevant pathways and present them on the page without any
need for user intervention. This can be extended to show all assertions in
the system that are semantically tagged with proteins in any shared
pathway, regardless of what disease areas they describe. This aids the
identifi cation of common pathways and potential synergies across
projects.
17.2.3 The product and user experience
To allow Pfi zer scientists to fully describe and present their hypotheses
and summaries, the assertions within the system are a mix of structured
data (Table 17.2, semantic tagging) and free-form text and images. The
semantic forms extension [38] provided a powerful and elegant
mechanism to structure this data entry. Figure 17.8 shows how an
assertion is created or edited.
The top of the edit form contains a number of drop-down menus
(dynamically built from vocabularies in the system) to enable users to
rapidly set the main properties for an assertion. Below this is the main
wiki-text editing area, using the FCKEditor plug-in that enables users to
work in a word-processor like mode without needing to learn the wiki
markup language. Next is the semantic tagging area, where assertions
can be associated with the objects of interest. Here, the excellent auto-
complete mechanism that suggests as one types is employed, allowing the
user to more easily enter the correct terms from supported vocabularies.
The user must enter the nature of the association ('Link' on the fi gure),
chosen from a drop-down menu. One of the most common links is 'Has
Actor', meaning that the assertion is associated with a molecular entity
that plays an active role within it. Finally, additional fi gures and references
can be added using the controls at the bottom of the page.
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