[Bioc-devel] Stability of biobase eSets/annotation

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Fri May 12 19:10:49 CEST 2006

> > Certainly annotation data changes over time and results will change
> > with it, but I don't think there is much we can/want to do about
> > that.  If you want the same results, use the same versions of the
> > annotation data.  If I've misunderstood, please feel free to explain
> > further.  I don't want to discourage suggestions or ways we can make
> > the software more useful. :-)
> I guess my more general point was that there are many (fairly complicated)
> data structures that undergo change over time besides those that contain the
> expression data.  When possible and when it makes sense, it might be
> beneficial to think about versioning and updateClass-type ideas for them as
> well.  The annotation packages might be candidates for that treatment.

Perhaps the distinction between structure and content can help
clarify these issues.  golubEsets is a package whose content is supposed
to be immutable, but the container structure changed in Biobase.  This
made it hard to use the old objects.  We want to simplify restoration
of old objects when externally defined structures change, and updateClass
is supposed to address this.

The annotation packages can change in structure, but the principal
aspect of change that we are concerned with is change in content.
Such changes arise as biological knowledge changes, and are basically
orthogonal to data structure design (bioc classes).

It does seem desirable to identify the version of an annotation resource
and to propagate that through the reporting workflow.  it would
be nice to have an object that could be updated with respect to
annotation content if new annotation environments came into being
after it was created.  An Sweave document that scripts the analysis
seems to be the closest thing we have to such an updateable object.
Swap in the new annotation and rerun.  Hopefully all the APIs are
unchanged; updateClass might even help in this situation if some
container structures changed in the mean time.  but it is -- under
current thinking -- independent of evolution of annotation content.

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