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Use of deprecated GO IDs in current gene association tables

fritz_roth frederick_roth at hms.harvard.edu
Fri Nov 16 05:57:51 PST 2001


Hi Karen,

Actually, deprecated is a term that I've really only heard in the context of 
computer languages.  I've understood it to mean, "destined for the trash heap 
but not quite there yet".

I asked good ole Dr. Google to tell me more about 'deprecated' and was led to 
a definition in the context of HTML:

---------------
from http://www.w3.org/TR/REC-html40/conform.html
Deprecated 
A deprecated element or attribute is one that has been outdated by newer 
constructs. Deprecated elements are defined in the reference manual in 
appropriate locations, but are clearly marked as deprecated. Deprecated 
elements may become obsolete in future versions of HTML. 
--------------------------------------------------

We may also want to pray against such terms, as an evil; to avert by prayer :)

Cheers,
Fritz


>===== Original Message From Karen Christie <kchris at genome.stanford.edu> =====
>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
>> -------------------------------------------------
>>
>> --
>> This message is from the GOFriends moderated mailing list.  A list of 
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-------------------------------------------------
Frederick P. Roth, Assistant Professor
Harvard Medical School
Dept. of Biological Chemistry and Molecular Pharmacology
250 Longwood Avenue, SGMB 322A
Boston, MA 02115
(617) 432-3551 phone
(617) 432-3557 FAX
froth at hms.harvard.edu
-------------------------------------------------

--
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