[Annotation] RefSeq / NCBI identifiers

[Alan Ruttenberg]

Note that a number of these URI's don't seem to work, e.g.

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NP_66919
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NP_4725
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_U34584
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NP_59819

One is malformed: (no _)

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=AC002324

Is there a policy to update to point to replaced record? For example,
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=XP_001068954 says
The record has been replaced by NP_001121125

I'd suggest being more explicit about what the possible XX are. For  
example, should we ever see gene annotation to a chromosome record  
(NC_)?
Also worth noting that the nnnnn... may be. Are they always digits.

As a consumer, it would be helpful to know under what circumstances  
each of the prefixes are used in annotation. i.e. what should we  
conclude when the annotation is to specific sequence versus model.

http://www.ncbi.nlm.nih.gov/RefSeq/key.html#accessions

Regards,
-Alan

On Jun 11, 2008, at 7:29 PM, Amelia Ireland wrote:

> Hello all,
>
> I have some more database references to be tidied up to standardize
> the way in which we refer to RefSeq accessions.
>
> The RefSeq syntax we recommend is
>
> RefSeq:XX_nnnnnnnnn
>
> e.g.
> RefSeq:NP_004597
> RefSeq:NM_000720
>
> This replaces several redundant methods currently used, such as
>
> NCBI_NP:066919
> NCBI_NM:NM_598961
> RefSeq_Prot:NP_808489
>
> and will enable us to provide stable links to the corresponding RefSeq
> entities.
>
> I've attached a tab-delimited text file with the entries in question  
> in
> it; all the refs appear in the 'with' column, and I have put in the
> suggested replacement value and the URL for the RefSeq entry that  
> would
> generated by AmiGO. You may want to check these refer to the correct  
> entry
> as a couple looked a bit dodgy.
>
> Thanks a lot!
> Amelia.
>
> -- 
> Amelia Ireland
> GO Editorial Office
> http://www.ebi.ac.uk || http://www.berkeleybop.org
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>
> <refseq_dbxrefs.txt>_______________________________________________
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