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

David Block dblock@gene.pbi.nrc.ca
Thu, 5 Apr 2001 11:31:19 -0600 (CST)

(cross-posted to biocorba as an invite)

On Thu, 5 Apr 2001, Hilmar Lapp wrote:

> Ewan Birney wrote:
> > 
> > <ewan's prejudice>
> > Annotation objects always seem to degnerate into something like name-value
> > pairs/multiple mix-in inheritance of interfaces. It is way too slippery to
> > pin down...
> > </prejudice>
> Hm. You mean there is no sensible AnnotationI a generic
> AnnotationDumper (like one dumping to GFF format) could be
> satisfied with? I of course don't know the past experiences with
> any attempts in this direction. (Does anyone have the BioJava
> solution at hand? Is there a IDL definition [BioCorba, BSA, ...]
> making an attempt at this?)
> 	Hilmar

I have been thinking about this rather hard lately.  We at PBI are
examining the possibility of an early fall conference in beautiful
Northern Saskatchewan (forests, lakes, wildlife, few tourists), inviting
'database people' from each of the major genome databases, to discuss
interfaces for comparing/exchanging/viewing deep annotation.  This
obviously overlaps with DAS (the shallow annotation network) and perhaps
BioCorba.  Costs are extremely reasonable (nothing at all like
Copenhagen), and we are working on a reasonable network connection, but no
promises there.

Anyone interested?  Over a weekend, with some time on Sunday for the kind
of fishing that brings people from all over the States?  (plus canoeing,
hiking, etc.)

We are looking to gauge support for this, in order to secure funding from
the suits.  Send email to me or Mark or both, and suggestions to the

> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                              email: hilmarl@yahoo.com
> GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
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Dave Block