[MOBY] Re: [MOBY-l] Name Space

[Boris Steipe]

On Wednesday, Feb 11, 2004, at 20:39 Canada/Eastern, Martin Senger 
wrote:

Point taken- but:

To my understanding, the LSID memo does not talk about the resolution 
*mechanism* at all - in the sense of specifying *how* a conforming 
query would need to be structured to be understood by the resolver.

So in practice the client will need to figure this out anyway. Since no 
mechanism is defined you can't use it in practice to resolve anything 
since you don't know how to structure a query. Human clients will go to 
the website, use the namespace to access the proper service and paste 
the acc to retrieve the data. Silicon clients will ... format it as a 
Moby query and send it to Moby  to have Moby resolve it for them? I 
guess thats the whole point here. The only thing that needs to be 
avoided is that the client is tricked into believing this is a real 
LSID, when it isn't. "urn:lsid" could either be optional (if present, 
assume there is a resolver, but you may want to use Moby anyway). Or 
one could use urn:biomoby_id:... to specify that Moby is the resolver 
but the namespace semantics are defined elsewhere. I guess it is not a 
Good Thing to use the same string to define both namespace and 
resolution protocol.

Bottom line: I suggest that Moby use LSIDs when available, create LSIDs 
only for objects that are truly Moby objects, require that all 
namespace be prefixed with an authority that defines that namespace's 
semantics and not define LSIDs for objects not under its semantic 
authority.

My concern would be that there might be a profusion of incompatible 
namespaces otherwise. After all, how would a client know that 
biomoby.org:pubmed has the same semantics as ncbi.nlm.nih.gov:pubmed . 
That strikes me as the larger Problem.

Not ?


Boris

> Just my 2c:
>    The authority field is not important only as a way how to identify
> things world-wide uniquely (if it was only for that, all your arguments
> are completely valid) - but it *may* (the LSID spec does not mandate 
> that
> but suggests it) be used also for finding an appropriate resolution
> service that can return data identified by this LSID. Therefore, if you
> put there pubmed.org, it may never find biomoby.org where it can be
> resolve.
>    I think the solution may be (Sean, are you listening here? Am I 
> right?)
> to have *both* in the authority - biomoby.org *and* pubmed.org - so the
> resolution software will find first biomoby.org and it knows that the 
> rest
> of the authority can be ignored.
>
>    Regards,
>    Martin
>
> -- 
> Martin Senger
>
> EMBL Outstation - Hinxton                Senger at EBI.ac.uk
> European Bioinformatics Institute        Phone: (+44) 1223 494636
> Wellcome Trust Genome Campus             (Switchboard:     494444)
> Hinxton                                  Fax  : (+44) 1223 494468
> Cambridge CB10 1SD
> United Kingdom                           
> http://industry.ebi.ac.uk/~senger
>
>



Best regards,


Boris

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



Best regards,


Boris

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