[Bioperl-l] GO annotatinos in BioPerl. A tentative proposal...

Jeffrey Chang jchang@SMI.Stanford.EDU
Thu, 5 Apr 2001 13:17:17 -0700 (PDT)

On Thu, 5 Apr 2001, Hilmar Lapp wrote:

> I can also easily imagine that there are other types of tree-like
> annotations, not necessarily restricted to sequences, e.g. for array
> data (tissue source, treatments, etc). I'd actually enjoy seeing an
> Annotation object (re)design that takes steps in this direction (i.e.,
> tries to abstract what can be abstracted on a reasonably low-pain
> level).

Absolutely.  There's two different things going on here: 1) representation
and computation on hierarchical ontologies like GO, and 2) annotating
sequences into 1.  Having a hierarchical data model represented explicitly
in code allows you to do very powerful queries.  For example, you could
ask, "Give me a list of all the sequences that are involved in signal
transduction" and receptor proteins would come up.  However, if you start
by putting too much GO information as sequence features, building tools
that will allow you to do this kind of inference is going to be hairy...

I urge you to keep the representation of GO separate from the annotation
on the sequence.  The sequence should contain only a very minimal
reference to an annotation, possibly as a perl pointer or a GO ID.