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[MISC] RE: [GO] Re: [MOBY] Re: GO Xref Abbs now served by MOBY

Mark Wilkinson markw at illuminae.com
Thu Feb 26 11:32:29 PST 2004


This actually brings up another point - a point that "smells" the same
as the point I made last week w.r.t. evidence codes.

At the moment, the Xref Abbs document has, e.g. "taxon" as a
cross-reference abbreviation for NCBI's taxonomy identifiers.  This then
precludes anyone else from using "taxon" as their namespace, even if
their database contains taxon identifiers (that may or may not be
identical to those of NCBI).  Sure, I agree that we should probably all
use the "taxon" identifiers as they are defined by NCBI, since theirs is
the ~canonical list... but what if someone suddenly registers "GeneID"
as a Xref Abb, with the intention that it means an identifier in the
potatoe genome database, or as in the message below!?!  From now on,
nobody will be allowed to use 'GeneID' as their namespace/Xref
abbreviation, so they will have to prefix it with e.g. TAIR_GeneID. 
That's fine and dandy, and in fact, at the computational level we don't
much care so long as there are no collisions... but it seems that the
Xref Abbs list was made without consideration of the scale that it might
grow to.  It would be nice to agree on a format for declaring these
abbreviations that ensures that we ENSURE that we avoid collisions.  The
most *obvious* and interoperable way to do this is to adopt the LSID
naming system, but that seems to be meeting with some resistance from
the other list members.  An alternative would be to either insist that
the Xref Abbs are prefixed with some vendor-specific tag (e.g.
NCBI_GeneID), or with their domain (ncbi.nlm.nih.gov:GeneID).  This
would allow multiple groups who have genes in their databases (i.e. most
of us!) to use the very generic "GeneID" namespace without stepping on
each others toes.

...just a thought...

Mark



On Thu, 2004-02-26 at 10:58, Maglott, Donna (NIH/NLM/NCBI) wrote:
> Although a date has not been set, NCBI plans to replace LocusLink with
> Entrez Gene.
> 
> The LocusID/URL is still valid:
> abbreviation: LocusID
> database:  NCBI LocusLink ID.
> object: Identifier.
> example: LocusID:3195
> generic_url: http://www.ncbi.nlm.nih.gov/
> url_example: http://www.ncbi.nlm.nih.gov:80/LocusLink/LocRpt.cgi?l=3195
> 
> But this also works and will apply to more genomes:
> 
> abbreviation: GeneID
> database:  NCBI Entrez Gene.
> object: Identifier.
> example: GeneID:3195
> generic_url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
> url_example:
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=grap
> hics&list_uids=3195
> 
> 
> NOTE: The value of the LocusID is conserved as the value of the GeneID.
> 
> -----Original Message-----
> From: Mark Wilkinson [mailto:markw at illuminae.com] 
> Sent: Thursday, February 26, 2004 11:19 AM
> To: Michael Ashburner (Genetics)
> Cc: gofriends
> Subject: Re: [GO] Re: [MOBY] Re: GO Xref Abbs now served by MOBY
> 
> 
> http://mobycentral.cbr.nrc.ca/cgi-bin/XrefAbbs
> 
> just click the link above to instantiate the cat... whether it is smiling or
> not will depend on the parse-test :-)
> 
> Attached is a saved version of the output from the script above as of this
> AM.
> 
> M
> 
> 
> On Thu, 2004-02-26 at 07:57, Michael Ashburner (Genetics) wrote:
> > Then can you instantiate the cat & send it (|her|him) to me. Keep the 
> > smile on its (|hers|his) face please. M
> > 
> > 
> > --
> > This message is from the GOFriends moderated mailing list.  A list of 
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-- 
Mark Wilkinson (mwilkinson at mrl.ubc.ca)
University of British Columbia iCAPTURE Centre

--
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