[DAS] DAS and bacterial genomes

Ewan Birney birney at ebi.ac.uk
Wed Aug 18 09:52:06 UTC 2010

>> I've brought in the three key people here on the EG side - Eugene  
>> (does the
>> web
>> side of this); Dan (main data production manager) and Paul Kersey  
>> (the EG
>> PI) -
>> some of them are on holiday now, but I suggest perhaps setting up a  
>> phone
>> conference (and/or Adam could you come for a visit?) to get this as
>> straight as
>> we can - I suspect there will both be short term fixes and more  
>> longer term
>> infrastructural fixes here.
> The DAS coordinate system scheme already handles multiple assemblies  
> for a
> given taxon fairly well (via the "authority" part).  So it sounds  
> like the
> main thing that's missing is a sensible way of distinguishing between
> strains.  Given that the CSs are already defined by XML elements with
> multiple attributes (many of them optional), would adding an (also  
> optional,
> of course) strain attribute get things 95% of the way there?

I dont think this quite works; the whole thing goes fractal here in  
that multiple
groups assign "their" assemblies to the same strain id so you have hte  
same problem,
just one level lower (I think).

At the last EBI/NCBI meeting we got to more clarity on there being  
tracking identifiers
for assembly series. I think this is the long term solution. But it  
needs to be pushed
out to bacteria, systems in place, and populated.

In the meantime we should do something practical to at least allow DAS  
servers to be
mounted against EG web sites (I think this is Adam's use case).

...but I am not the expert here. Each time I think this is simple  
it .... doesn't end up
that way.

>               Thomas.
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