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Use of deprecated GO IDs in current gene association tables

Karen Christie kchris at genome.Stanford.EDU
Thu Nov 15 16:56:54 PST 2001


Hi Fritz,

Thanks. I'll look into the SGD one. 

Could I also ask you to clarify exactly what you mean by 'deprecated'?
Being completely unfamiliar with this word, I've just heaved the massive
dictionary onto my desk and am really intrigued now, having read the
variety of definitions given for 'deprecate':
	1. to pray against, as an evil; to avert by prayer
	2. to express disaproval of
	3. (obs.) to supplicate or beseech; to invoke

Presumably you meant 'obsolete' and/or 'secondary', rather than
'deprecated', though I suppose there is some disapproval involved in
continuing use of 'secondary' IDs.

Anyway, having let my jet-lagged brain wander off into the tangent of the
definitions of 'deprecate', I'll look into the SGD one. Thanks again for
catching these.

Cheers,

-Karen

On Thu, 15 Nov 2001, Fritz Roth wrote:

> Hi All,
> 
> In the latest version of sgd, mgi, and fb gene association tables from
> ftp://ftp.geneontology.org/pub/go/gene-associations/ there is the use of 
> one or more deprecated GO IDs:
> 
> In gene_association.fb
> The following deprecated IDs are used:
> 0003710
> 0019006
> 0017167
> 0016940
> 0008461
> 0018999
> In addition there are three cases where a GO ID has a typo (extra '0'):
> 00058924
> 00036763
> 00057622
> 
> In gene_association.sgd
> The following deprecated ID is used:
> 0015237
> 
> In gene_association.mgi
> The following deprecated ID is used:
> 0006632
> 
> Thanks!
> Fritz Roth
> -------------------------------------------------
> Frederick P. Roth, Asst. Professor
> Harvard Medical School
> Dept. of Biological Chemistry and Molecular Pharmacology
> 250 Longwood Avenue, SGMB-322, Boston, MA 02115
> (617) 432-3551 phone            (617) 432-3557 FAX
> froth at hms.harvard.edu           http://llama.med.harvard.edu
> -------------------------------------------------
> 
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