[MOBY-l] Re: bioMoby - name space (fwd)

[Martin Senger]

These are some opinions on the name space problem we had discussed in this 
list from the main LSID promoter/author, Sean Martin from IBM. I am 
expecting other email from him regarding "faking" the authority field - I 
will post it when I have it...

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

---------- Forwarded message ----------
Date: Thu, 12 Feb 2004 09:27:17 -0500
From: Sean Martin <sjmm at us.ibm.com>
To: Martin Senger <senger at ebi.ac.uk>
Cc: Boris Steipe <boris.steipe at utoronto.ca>, markw_mobile2 at illuminae.com,
     Benjamin H Szekely <bhszekel at us.ibm.com>, Alyssa Wolf <alyssaw at us.ibm.com>,
     Jordi A Albornoz <jordi at us.ibm.com>
Subject: Re: bioMoby - name space

Hi Martin,
The way we have being thinking about it here is as follows (this is not to 
say it could not be extended as things move forward of course):

Take a lsid  ->  urn:lsid:pdb.org:1aft-qwertyfoo:1 

In this case, when I resolve it, I get pointers to the data named by the 
LSID as well as any meta-data that may be associated with it from the PDB. 
The rule we have followed is that the only authoritative place to get data 
(actual bytes named) for that LSID would be the owning authority - in this 
case the PDB. However *any* resolver (including the PDB) may have also 
have pointers to meta-data related to that LSID.  Each organization that 
has meta-data is authoritative for the meta-data that it supplies. It is 
up to the client that retrieves meta-data to decide what weight (i.e. just 
how good is this meta-data?) to give a piece of meta-data depending on 
which authorities (the source of that bit of meta-data) provided it to 
them.  Naturally the weight for meta-data from the authority that actually 
is authoritative for the data would be high - although perhaps not as high 
as my own local database which gives me the information that in my own 
testing I (for instance) found an error in the official/original 
authorities data/meta-data. The client is free to ask any number of 
authorities (there is no mechanism yet for the discover of these third 
party resolvers - you just have to know them) if they have meta-data for 
any particular LSID. Meta-data from third part authorities is usually not 
the same meta-data that the "original naming" authority (in this case the 
PDB) lists for that LSID. So biomoby.org is quite at liberty to hold its 
own meta-data records for pdb.org or any other authority issued ID's. 
Biomoby clients would be programmed to know to query both the actual 
authority listed in the LSID and the biomoby resolver any time LSID 
resolution is performed. 

This mechanism allows third parties to attach meta-data/or otherwise 
assert facts about data stored in another authority e.g annotation.  In 
fact in our LSID resolver proxy implementations, I believe you can supply 
a list of 3rd party resolvers that you want queried any time an LSID is 
resolved. This allows things like checking a bunch of internal databases, 
or the databases of "friends & colleagues" or other source important to 
your research, for data related to any LSID you happen to be resolving.

I hope this is reasonably clear. Please ask questions if not.

Kindest regards, Sean
:








Martin Senger <senger at ebi.ac.uk> 
02/12/2004 04:18 AM

To
Sean Martin/Cambridge/IBM at IBMUS
cc
Boris Steipe <boris.steipe at utoronto.ca>, <markw_mobile2 at illuminae.com>
Subject
bioMoby - name space






Sean,
Yesterday there was a discussion on the BioMoby list about authority
field of the LSID - just in case you are not on that list, here is a very
brief summary - because I have asked there for your expertise:

1) Boris asked:

"What happened to the idea of namespacing like in LSIDs i.e. making a
namespace valid only in the context of its issuing authority and thus
effectively using the (working, sort of) ICANN resolution mechanism to
ensure that namespaces remain unique ?"

2) Mark replied:

"yes, that was the plan... and in effect it still *is* the plan. However,
I cannot assign LSID's arbitrarily to another authority (this is something
they must do on their own), so for the moment all namespace identifiers
are in the "biomoby.org" LSID authority, and thus we have to be careful of
collisions.
Once LSID's become more widespread we will certainly stop using our own
LSID authority prefix and use the "genuine" one, as assigned by the true
naming authority, but until then... we're stuck."

3) I have said:

"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.
"

4) Finally Mark concluded:

"Cool - that's a trick I hadn't known about.  What is the separator
character between the two authority identifiers?"

Now, Sean, your opinion? Many thanks,
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