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

David Block dblock@gene.pbi.nrc.ca
Thu, 5 Apr 2001 15:10:43 -0600 (CST)

On Thu, 5 Apr 2001, Jonathan Epstein wrote:

> I strongly agree
> - Jonathan
> At 04:17 PM 4/5/2001 , Jeffrey Chang wrote:
> >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.

In theory, this is great.  However, if you are annotating 'tentatively'
and you are not ready to submit an annotation to the GO curator for your
organism, where do you put the evidence you are assembling?  Once you have
the argument straight in your head, it should become part of the official
GO ontology database, and the link can go from the GO annotation to your
transcript, as served via DAS or HTML.  You can also then put a link from
your transcript to the GO database.

Until that point, we need a place to store 'provisional' annotations.
That is what this Annotation object is for, in my view.

> Jonathan Epstein                                Jonathan_Epstein@nih.gov
> Head, Unit on Biologic Computation              (301)402-4563
> Office of the Scientific Director               Bldg 31, Room 2A47
> Nat. Inst. of Child Health & Human Development  31 Center Drive
> National Institutes of Health                   Bethesda, MD 20892
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