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Use of deprecated GO IDs in current gene association tables

Michael Ashburner (Genetics) ma11 at gen.cam.ac.uk
Fri Nov 16 07:10:22 PST 2001


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
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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
> -------------------------------------------------
> 
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