[DAS] [DAS2] [Fwd: Re: Writeback implementation]

[Garret Wilson]

Gregg Helt wrote:
> So let me rephrase.  Every feature in DAS/2.0 has a unique URI.  In 
> the feature XML this is represented by the "uri" attribute of the 
> FEATURE element, which is a URI reference (URI or relative URI 
> reference), and optional xml:base attributes in the document.  DAS/2.0 
> uses the XML Base specification <http://www.w3.org/TR/xmlbase/> to 
> resolve relative URI references via xml:base attributes and/or the URI 
> the document is a representation of. 

Sounds like we're all on the same page, then.

This brings up a related issue regarding the assembly and sequence URIs 
at http://www.biodas.org/wiki/GlobalSeqIDs . Before on this list I've 
brought up the issue of whether DAS has authority to maintain 
identifiers in namespaces from domains controlled by third parties (i.e. 
NCBI). This still worries me.

How confident can we be that the DAS GlobalSeqIDs are stable and will 
not change for a while?

Secondly, related to URI resolution, I note that I cannot take an 
assembly URI such as http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B36.1/ 
and simply resolve the chromosome ID (e.g. chr1) against it to form the 
sequence URI. My application instead has to have specific knowledge of 
this particular assembly namespace, knowing that it must first append 
the path segment "dna/" to the URI, yielding 
http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B36.1/dna/chr1 .

I'd rather my application, once it knew the assembly URI, simply need to 
resolve the chromosome ID to the assembly URI to determine the sequence 
URI, such as http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B36.1/chr1 .

Garret