[MOBY-l] Re: MOBY LSID's

[Boris Steipe]

On Thursday, Feb 12, 2004, at 09:54 Canada/Eastern, Mark Wilkinson 
wrote:
[...]
>
> The important point that I think is being misunderstood here is that we
> are talking about LSID's that *represent namespaces*, NOT LSID's that
> represent data within that namespace!!  As such, biomoby.org is
> *absolutely* the correct authority for namespace LSID's, since
> biomoby.org controls the namespace ontology (as of last week!).

Ok. Thanks! This clarifies my misunderstanding. And I won't harp on the 
aspect of resolution because it's beside this point. Even though I 
believe implicit behavior is never a Good Thing, like LSID sort of 
implying a resolution mechanism. Brrr.

But back to Vijay's original namespace request for IND, bib ... : 
registering not the namespace but the namespacetype doesn't solve the 
problem but moves it to a metalevel.

I understand you would register

    urn:lsid:biomoby.org:namespacetype:IND

But this inherits the problem, it would require something like the 
following to be unique.

urn:lsid:biomoby.org:namespacetype:agricola.cos.com<some separator 
here>IND

... or do I still not get it ?


Boris

>
>
> I discuss this point in various places, but in particular it is
> discussed in my latest paper (get it from the biomoby.org website).  In
> there I have a paragraph clarifying the problem that MOBY has with 
> using
> LSID's "verbatim" (the crux being that LSID's are opaque and DO NOT
> represent underlying data-types without resolution - where the 
> knowledge
> of the underlying data-type is critical to service discovery).  I think
> we are confusing the issue by conflating an identifier WITHIN a
> namespace - for which Boris' argument is absolutely correct and I don't
> think anyone could argue with him - with an identifier that REPRESENTS 
> a
> namespace, for which MOBY is the only authority that exists.
>
> urn:lsid:biomoby.org:namespacetype:DragonDB_Allele
>
> vs.
>
> urn:lsid:antirrhinum.org:allele_id:AG113328
>
> I believe that this is the misunderstanding that is leading to this
> argument, and that once this is clear, the argument goes away.  If not,
> then please read my paragraph about it in the manuscript as I deal with
> it more comprehensively there.
>
> If you all could give me the OK I will forward this message back to the
> public list and we can finish the conversation there.
>
> Thanks!
>
> Mark
>
> -- 
> Mark Wilkinson <markw at illuminae.com>
> Illuminae
>



Best regards,


Boris

---
Boris Steipe
University of Toronto
Program in Proteomics & Bioinformatics
Departments of Biochemistry & Molecular and Medical Genetics
http://biochemistry.utoronto.ca/steipe/