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

Steve Chervitz Steve_Chervitz at affymetrix.com
Thu Mar 6 20:21:59 UTC 2008

Hi Garret,

As mentioned on the GlobalSeqIDs page:

"The URLs do not need to be resolvable. At this point they are abstract

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:

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

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.

Anyone else have thoughs/suggestions?


> 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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