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

Suzanna Lewis suzi at fruitfly.org
Thu Feb 26 12:09:04 PST 2004


I agree that the LSID would be the way to go (no sense knocking
heads if we can avoid it). But I think many people on the list may
not be all that familiar with what the ACRONYM "LSID" means
in concrete terms. Would you send out a lay-person's description.
I think it really is a simple thing that looks gussied and complex
because it has an acronym.

-S

Mark Wilkinson wrote:

>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
>>>
>>>
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>>>

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