[DAS2] approval and maintenance of DAS/2 URI namespaces

Chris Mungall cjm at fruitfly.org
Thu Mar 6 22:02:18 UTC 2008

On Mar 6, 2008, at 12:21 PM, Steve Chervitz wrote:

> Hi Garret,
> As mentioned on the GlobalSeqIDs page:
> "The URLs do not need to be resolvable. At this point they are  
> abstract
> identifiers."
> So they just happen to use ncbi, flybase, wormbase, etc. servers.  
> In one
> sense, it doesn't matter what they are so long as all DAS servers that
> provide data for these assemblies consistently use them.
> To my knowledge, none of these organizations know that we are using  
> their
> URI namespace in this way (except maybe for wormbase, which Lincoln  
> -- who
> came up with these IDs -- works with). Is this a weakness? Perhaps.  
> It's
> more a sign of the fact that most organizations are not yet clued  
> into DAS.
> This issue harkens back to the URL-vs-URN-as-URI debate and whether  
> URIs
> should be opaque, for example:
> http://rest.blueoxen.net/cgi-bin/wiki.pl?RestAndUriOpacity

The debate has been raging on and off on various semantic web mail  
lists over the years as well. Particularly the public-semweb-lifesci  

The consensus appears to be URLs over non-URL URIs (though consensus  
is not necessarily right), though Mark W (guessing you're on this  
list Mark?) and others favour LSIDs.

> DAS has been designed with RESTful principles, so the abstractness
> requirement of the global seq IDs may seem unexpected.

The consensus within the URL camp is that URLs should resolvable.

So the DAS/2 approach of using URLs for which it would be difficult  
to guarantee resolvability would appear to be out of step with both  

> I can see some advantages of using the biodas.org namespace for these
> identifiers. The DAS maintainers would then be in control of  
> managing any
> potential resolvability requirements.
> But given that we've already published these global seq IDs, I  
> don't know
> the best route to change them should we decide to do so. If we  
> published
> biodas.org-based URIs as synonyms to the current IDs, existing DAS/ 
> 2 servers
> and clients (of which there aren't many yet) would need to be  
> updated as
> well, to know that http://www.ncbi.nlm.nih.gov/genome/H_sapiens/ 
> B33/ is
> equivalent to http://biodas.org/genome/H_sapiens/B33/, for example.

My feeling is that officially granted identifiers such as NC_000001.9  
(current build of H_sapiens chr1) should be used where possible, with  
URIs constructed using some external registry of databases; eg

However, there is clearly a need for a RESTful way of referring to  
sequence assemblies keyed by organism, build and chromosome, along  
the lines mentioned above. This could be a useful service of biodas.org

I'm not sure if some notion of URI synonyms is built into DAS/2. This  
could perhaps be done externally via URL redirects and/or RDF metadata

> Anyone else have thoughs/suggestions?
> Steve
>> From: Garret Wilson <garret at globalmentor.com>
>> Organization: GlobalMentor, Inc.
>> Date: Fri, 29 Feb 2008 10:31:12 -0800
>> To: <das2 at lists.open-bio.org>
>> Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces
>> I read the "list of global identifiers based on community  
>> consensus" at:
>> http://www.biodas.org/wiki/GlobalSeqIDs
>> It's great the DAS/2 is using URIs for global identification. For
>> example, chromosome 1 for the B36.1 human genome assembly is  
>> identified
>> by the URI:
>> http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B36.1/dna/chr1
>> I'm unclear, however, regarding NCBI knowledge, participation, and
>> maintenance of these URIs. The system of uniform resource identifiers
>> prevents name clashes by delegating to the IANA-governed domain-name
>> system, so that whoever owns a particular domain-based namespace can
>> manage the URIs within that namespace.
>> If DAS/2 were to use, for example, the http://www.biodas.org/genome/
>> namespace to manage all genome assembly URIs, I would have no  
>> cause for
>> concern. DAS/2 is instead using several namespaces managed by other
>> parties. I hope the response is that the NCBI is fully aware that its
>> URI namespace is being used as authoritative genome assembly URIs and
>> has either committed to maintaining that namespace or has delegated
>> maintenance of the http://www.ncbi.nlm.nih.gov/genome/ namespace  
>> to DAS.
>> (If the latter is true, it is unclear which organization would  
>> receive
>> such a delegation of maintenance responsibility---the Open
>> Bioinformatics Foundation? The BioTeam?)
>> Thanks for any clarifications---this question is raised solely out  
>> of a
>> desire for long-term standards that can be use consistently by the
>> community.
>> Garret
>> _______________________________________________
>> DAS2 mailing list
>> DAS2 at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das2
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