[DAS] standard entry_points

[Lincoln Stein]

Yes, on a per-organism basis I agree completely on an entry point naming 
convention.  This has to be done in such a way as to match what the community 
is already doing.  The C. elegans community uses roman numerals, whereas the 
fruitfly community uses arms (e.g. 2L)

I will start with the following:

	Human		1, 2, 3... X, Y, Mit
	Mouse		1,2,3...19, X, Y, Mit
	Fruitfly		2L, 2R, 3L, 3R, 4, X, Mit
	C. elegans	I, II, III, IV, V, X, Mit
	S. cerevisiae	I, II, III.... XVI, Mit
	Rice		1, 2, 3......12, Mit, Chlor
	A. thaliana	1, 2, 3....5, Mit, Chlor

I've removed the CHROMOSOME_ from the WormBase DAS server, since that's a 
WormBase thing and not a community thing.

Lincoln


On Tuesday 19 March 2002 18:40, Brian wrote:
> Hmmm...
>
> 	I'm not sure we are on the same wavelength here. I will outline
> the problem that we are experiencing more completely:
>
> 	We have found that each implementor of the DAS spec has come up
> with his/her own way of representing the concept of an "entry_point". The
> spec loosely defines these entities and as such provides a lot of room for
> interpretation. The Dazzle implementors can jut pick the contigs out of
> the ensembl schema and serve these up. Wormbase calls their chromosomes by
> a naming convention such as "CHROMOSOME_I". Other Human DAS reference
> servers "or annotation servers" just provide a "1" or "2". This is
> insufficient for us to be able compare the semantic meanings of these
> entities across different servers so that we can make sure that we are all
> talking about the same entry_point. While we could always come up with a
> huge DB of tuples that map all these semantic relationships, wouldn't it
> be better to have a published specification that allowed all implementors
> of the DAS specification to publish entry_points in a machine readable
> way?? Is this not one of the main points of a DAS like system??
>
> 	I propose that we try and standardize our entry_points naming
> conventions on a per organism basis. This way we can give a DAS client a
> reasonably good chance at figuring out if two servers are talking about
> the same place in the genome. Perhaps we can just settle on th top level
> entry_points and allow our software systems to do a quick and dirty
> nucleotide check to figure out if they are really the same thing under the
> top level entry_point??
>
> 	How do others feel about this??
>
>
> 					-B
>
> On Tue, 19 Mar 2002, Matthew Pocock wrote:
> > John Mayer wrote:
> > > Wouldn't it be helpful if the DAS spec  included standard
> > > top level entry_point names for the most common species
> > > so DAS clients didn't have to scramble around  a needless
> > > variety of labels like    chr1  CHR1  1   etc.   ?
> > > John Mayer
> > >
> > > _______________________________________________
> > > DAS mailing list
> > > DAS@biodas.org
> > > http://biodas.org/mailman/listinfo/das
> >
> > Or perhaps richer descriptive data associated with the entry points?
> > Perhaps even some structured descriptive data?
> >
> > ;-)
> >
> > M
> >
> > _______________________________________________
> > DAS mailing list
> > DAS@biodas.org
> > http://biodas.org/mailman/listinfo/das

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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