[MOBY-l] thinking about provision info and authoritative service providers

[Mark Wilkinson]

Exactly.

I need to learn to be more consice :-)

M


Lincoln Stein wrote:
> The LSID view is that there is an authority for a namespace.  That is, only 
> NCBI is allowed to give a GenBank ID to a sequence entry.  We need to 
> distinguish between who has the right to associate a recognized name with a 
> data object, and who has the right to perform computations on it and to 
> aggregate objects in various ways.
> 
> 
> Lincoln
> 
> On Friday 25 October 2002 01:51 pm, Mark Wilkinson wrote:
> 
>>Hi everyone,
>>
>>There are a bunch of thoughts crystallizing in my mind at the moment
>>around issues of provision information and versioning and such.  It has
>>come up repeatedly as I give the MOBY presentation in various places,
>>and is clearly something that scientists are very concerned about right
>>from the get go.  In addition, the good folks at myGrid have seen it as
>>sufficiently important that it is a major part of their entire platform,
>>whereas we have largely "put off" the problem.
>>
>>This was all brought to the surface yesterday during a telephone
>>conversation with Lincoln, Damian, Andrew, et. al..  The issue came up
>>of "who gets to serve", for example, GO_Terms.  It wasn't phrased that
>>way, of course, but that was in some ways the essense of the issue.
>>
>>Given that we put no restrictions on who may provide whatever service,
>>it is possible (likely!) that many services will be providing outdated
>>information. Lincoln suggested that we perhaps flag certain bodies as
>>being "authoritative". A few tweaks to the MOBY Central database and API
>>would be sufficient to store this information and also limit requests
>>to, for example, "authoritative services only".
>>
>>...but this opens up some questions in my mind... apart from the
>>political jockying about who gets to *be* authoritative and on whose
>>head that decision is going to fall ;-)
>>
>>I was thinking about the use of the word "authority" in the MOBY versus
>>LSID world.  In both cases, we represent the "authority" as a URI
>>effectively naming an organization.  However, in LSID the authority is
>>(in my interpretation of the spec) tightly linked to a namespace, while
>>in the MOBY world the authority is tightly linked to a service.  So LSID
>>folks might intuitively believe that the authoritative server for the
>>Genbank namespace is NCBI, while in MOBY this is not always going to be
>>the case... for example, if the Gene Ontology consortium decides to set
>>up a service that takes in GO_Terms and spits out GenBank records of
>>sequences in GO that are annotated to that term... then they are,
>>clearly, the authoritative providers of GenBank in that circumstance,
>>since they have the most up-to-date information on the
>>**transformation** that they are providing.  This leads us to a somewhat
>>peculiar situation where we could ask "who is the authoritative provider
>>of Genbank records" and both NCBI and GO appear as the answer.  Of
>>course, the truth is that NCBI is the authoritative transformer of
>>GenBank GI's or Accessions into GenBank records, while GO is the
>>authoritative transformer of GO/ID's into Genbank records... but it is
>>still a bit peculiar.  I don't know if it is going to be problematic in
>>the end, but it is something to keep in mind as we move towards adoping
>>authoritative services....
>>
>>The other thing that directly relates to this is versioning information.
>>  Whether you are using the authoritative service or not, you still want
>>to know the version of the resources (both data and software) that are
>>being provided to you.  Again, because our services (under the current
>>MOBY architecture) are generally unrestricted, this might be confusing,
>>but at least we seem to have a place to fit this information.  The
>>underused <MOBY/> envelope isa natural place to stick this
>>information... perhaps as attributes of the MOBY envelope
>>
>><MOBY authority="geneontology.org" GenBank="version xx"
>>GeneOntology="version yyy" authoritative="yes" Date="12-12-02 13:05:02">
>>
>>	<Sequence namespace="Genbank/GI" id="123456">
>>		...
>>		...
>>	</Sequence>
>>	<Sequence namespace="Genbank/GI" id="789012">
>>		...
>>		...
>>	</Sequence>
>></MOBY>
>>
>>
>>I realize that the vocabularies for the resources aren't controlled, but
>>we can hopefully find a way to deal with that...  nevertheless, is that
>>just too ugly, or do you think that is sufficient to accomplish what is
>>needed?  It certainly is a simple solution...
>>
>>Philip/Carol/Robert - how do you represent this data in myGrid?  Have
>>you found that there a need to be more complicated than that?
>>
>>M
> 
> 


-- 
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"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson, RA Bioinformatics
National Research Council, Plant Biotechnology Institute
110 Gymnasium Place, Saskatoon, SK, Canada

phone : (306) 975 5279
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