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Use of deprecated GO IDs in current gene association tables

Karen Christie kchris at genome.Stanford.EDU
Mon Nov 19 12:20:39 PST 2001


Hi Fritz,

Thanks again for excellent error catching. We've updated the script that
writes the gene_association.sgd file to write to the correct location in
the cvs repository. The script runs nightly, so you should be able to
get the most up-to-date versions of SGD's gene associations again.

Cheers,

-Karen


On Fri, 16 Nov 2001, fritz_roth wrote:

> 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 A deprecated element or attribute is one that has been outdated by newer 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 
> public
> >> announcements and discussion of the Gene Ontology (GO) project.
> >> Problems with the list?           E-mail: owner-gofriends at geneontology.org
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> >> Web:          http://www.geneontology.org/
> >>
> 
> -------------------------------------------------
> 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
> -------------------------------------------------
> 
> --
> This message is from the GOFriends moderated mailing list.  A list of public
> announcements and discussion of the Gene Ontology (GO) project.
> Problems with the list?           E-mail: owner-gofriends at geneontology.org
> Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
> Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
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> 

--
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