[DAS] standard entry_points

[Paul Gordon]

> Within a particular organism's genome, the entry points should be the same 
> (they are defined by the reference server).  Perhaps I'm missing something, 
> but what is the point of using the same nomenclature for C. elegans 
> CHROMOSOME_I and human Chr1, since you would never jump from one to the other 
> on the basis of the name alone?
If it's in the spec though, and suppose two people start writing DAS
servers for Mastigamoeba balamuthi.  They might choose different entry
point names off the bat, since there aren't any out there already, then
they'd have to reconcile. Is there a particular advantage to letting
people use roman numerals, etc. at the cost of naming conflict for new
services?

It might also be advantageous for browsers to be able to recognize top
level entrypoints as they map to physical phenomona in a standard way...
 
> Lincoln
> 
> On Tuesday 19 March 2002 19:22, Paul Gordon wrote:
> > This may be a naive approach, but can you not use a standard conventions
> > that would work across organisms?  E.g.  the DAS specification could say
> > something along the lines of
> >
> > "The top level entry points, when refering to the distinct DNA units in a
> > cell, an implementation shall use the conventions:
> >
> > Chromosome x
> > Where x is a decimal number (e.g. 1 or 23), X or Y
> >
> > Plasmid x
> > Where x is the name of the plasmid in GenBank, if available
> >
> > Extrachromosomal element x
> > ...
> >
> > "
> > That would at least make the standard cases straightforward.
> >
> > My CAN$0.02 worth...
> >
> > ----------------------------------------------------
> > Purgamentum init, exit purgamentum
> >
> > Paul Gordon
> > Research Associate
> > University of Calgary
> >
> > On Tue, 19 Mar 2002, 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
> > > >
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> > >
> > > --
> > > ----------------
> > > Brian Gilman <gilmanb@jforge.net>
> > >
> > >
> > >
> > >
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> 
> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein@cshl.org			                  Cold Spring Harbor, NY
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