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Rama Balakrishnan rama
Fri Nov 16 15:19:42 PST 2001


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Date: Fri, 16 Nov 2001 18:09:45 -0500
To: Michael Ashburner (Genetics) <ma11 at gen.cam.ac.uk>
From: Fritz Roth <froth at hms.harvard.edu>
Subject: Re: Use of deprecated GO IDs in current gene association tables
Cc: gofriends at geneontology.org
In-Reply-To: <E164kdK-0001OJ-00 at ma11.gen.cam.ac.uk>
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Hi Michael,

Your earlier email of Sept 27 said that the typos and deprecated IDs I 
mentioned had been fixed at that time.  That the errors are still in the 
current gene_association.fb file at the GO web site makes sense, if the 
file on the GO web site has not been updated since Sept 27.

If it has been updated more recently, then this may be more than an 
asynchrony problem?

Thanks,
Fritz

At 03:10 PM 11/16/2001 +0000, you wrote:
>Fritz
>
>I have just checked the FB files here in Cambridge and none of the
>problems remain.  There is always going to be an asynchrony problem
>between the GO tables and the gene_association tables.  At least now FB 
>produces
>the g_a table about once a month yet the GO atbles get u/dated in real time.
>
>There could be some way of obviating these problems, eg all the collaborating
>d/bases only using the files that GO freezes montly, but that may be hard
>to implement given the "autonomy" of the model organism databases.
>
>Of course, we are always happy to receive notification of errors.
>
>Best
>
>Michael
>
>
> > From owner-gofriends at genome.stanford.edu Fri Nov 16 00:20:29 2001
> > Envelope-to: m.ashburner at gen.cam.ac.uk
> > Delivery-date: Fri, 16 Nov 2001 00:20:29 +0000
> > X-Authentication-Warning: alberich.Stanford.EDU: majordom set sender to 
> owner-gofriends at genome-mail.stanford.edu using -f
> > X-Sender: frederick_roth at hms.harvard.edu
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> > Date: Thu, 15 Nov 2001 18:57:13 -0500
> > To: gofriends at geneontology.org
> > From: Fritz Roth <froth at hms.harvard.edu>
> > Subject: Use of deprecated GO IDs in current gene association tables
> > Mime-Version: 1.0
> > Sender: owner-gofriends at genome.stanford.edu
> >
> > 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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> >
>
>--
>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
>Web:          http://www.geneontology.org/

-------------------------------------------------
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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