[DAS] standard entry_points
Lincoln Stein
lstein@cshl.org
Thu, 21 Mar 2002 15:34:19 -0500
People working on unfinished genomes are going to want to use golden path
contigs, and so on, not chromosomes. I think it's best if we let the
species-specific sites figure out what works best for them.
Lincoln
On Thursday 21 March 2002 13:51, Paul Gordon wrote:
> > 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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--
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Lincoln D. Stein Cold Spring Harbor Laboratory
lstein@cshl.org Cold Spring Harbor, NY
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