Doh!! Re: [MOBY-l] Hmmm... ID objects or SpecificID objects??

[mwilkinson at gene.pbi.nrc.ca]

As usual, I was too thick to understand what Suzanna/Jason were saying
in this thread.  Sorry!  This issue
came up again in a conversation I had with Luke in the pub last week and
I
finally realized what the problem is:  that we don't distinguish between
"cross-references" and "synonyms" in our current object structure.  I
think we (I) had originally intended to put synonyms into the
CrossReference
block, but I'm not so sure that is a good idea now that I think about it
again...  it could result in the
same piece of data being retrieved twice.  Yet it is important to pass
the synonyms back along with the object if they are known since
different servers will use different namespaces.

perhaps a synonyms block in addition to a cross-reference block would be
useful?  This also solves Jasons concern about services being agnostic
to
namespace (which they are already allowed to be, under the MOBY Central
registration system inany case, but this reinforces that...)

Other ideas?  I'd like to clarify this by early next week before I
submit
the BIB manuscript...

M



Mark Wilkinson wrote:

> Suzanna Lewis wrote:
>
> >     it would be useful to have both available.
> >      e.g.
> >      <ComplexSeq auth="blah" namespace="diblah" id="whatever">
> >          <external_ref>
> >             <authority>TIGR</authority>
> >             <for-db>arabidopsis</for-db>
> >             <id>11111</id>
> >         </external_ref>
>
> I think this was the intention of the CrossReference (formerly known as
> "MIB") block that is associated with each object.  The object has it's
> primary identifier in it's Triple and then all cross-references that the
> Distributor knows about are in the CrossReference block as a list of
> xref'ing Triples.
>
> > then egg-on-my-face and sorry and all that.

--
--------------------------------
"Speed is subsittute fo accurancy."
________________________________

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

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