Databases and Systems

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Experimentally determined gene-expression patterns will come from embryos that
may not match the defining criteria for a particular stage because of inter-strain
differences or simply natural variation and the embryos may not have been staged
using the Theiler system. In this situation the data will be submitted with the authors’
best estimate in whatever staging system used, and kept so that a user can be aware of
how the stage was estimated. For search, that temporal information will be converted
to an equivalent Theiler stage range, since in general there may not be sufficient
precision to determine a single corresponding Theiler stage. The transformation
between different staging systems is encapsulated in the table published by Bard et al
(1998) 1 and is reproduced on the WWW pages of the Mouse Atlas Project
(genex.hgu.mrc.ac.uk) and shown
graphically in figure 3.
Viewing Coordinates
To accommodate the finer
grain descriptions of the
development sequence provided
by Downs and Davies [17] for the
early embryos, the “integer”
Theiler stages have been extended
to “floating-point” thereby
defining sub-stages in the Theiler
system.
Figure 4: Edinburgh Mouse Atlas
section viewing coordinates. The
fixed point can be redefined as
required
To submit data to the database or to make queries involving spatial coordinates the
user must be provided with an interface in which to define spatial position or region.
The simplest interface appropriate to this task presents the user with a section view
¹ Submitted to Development.