[DAS2] DAS/2 weekly meeting notes for 14 Nov 05

[Andreas Prlic]

Hi!

I realized there were a couple of questions regarding the way 
"coordinate systems"
are defined in the DAS-registry, so it would have been good if I would 
have joined yesterday....
I am glad that the conference is now at a time which is better for us 
europeans and want to join
in future for some of the topics like registry, coordinate systems, 
proteins, etc.


>
> AD: ebi/sanger tracks three fields related to assembly (what they need
> per server):
> -authority  = equiv to our assembly uri
> -organism   = we have as taxon
> -type       = ?


"type" refers to a "physical dimension" of an object. E.g. a 
chromosome, a 3D protein structure, a protein sequence.


>
> Permits people to query things like: find out all servers that offer 
> ncbi
> build 35 for human.
>
> Question: What do they mean by 'coord system'? some confusion here
> e.g., Do they mean things like: 'this assembly start at 5000 relative
> to this other assembly'?

no, as Thomas already mentioned these "coordinate systems" could also 
be called "namespace".
They should be globally unique descriptors for reference objects / 
databases.


>
> For protein DAS, authority typically defines two diff coord systems:
> 'pdb resnum, interprot'

> It does not permit automated translation between two coord systems.

unfortunately this is not that easy in protein space. The mapping from 
the 3D protein structure to the protein
sequence is not straightforward. Think of negative, non-consecutive, 
and "non-numeric" residue numbers
  that can appear in the 3D structures. Therefore we came up with the 
"alignment" DAS - document that allows to map one object in one 
coordinate system to another one. it can also be used to map one 
assembly to another.


> [A] - Andrew will find out what they use it for
>
> AD: Believes the purpose is intended for human consumption.

not only - the DAS clients usually can display a certain "coordinate 
system" e.g. Ensembl can do
Chromosomal ones, but if DAS sources are available that speak the 
"UniProt, Protein Sequence" coordinate
system, it knows how to project these onto the genome. - an 
"intelligent DAS client" :-)


Andreas

-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
			 +44 (0) 1223 49 6891