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Use of non-primary GO IDs in gene association tables

Karen Christie kchris at genome.Stanford.EDU
Wed Sep 26 15:21:24 PDT 2001


Hi Fritz,

Thanks for picking up those secondary IDs in the gene_associations
file. As you note, they shouldn't be there. I'll take care of the SGD
ones.

Cheers,

-Karen


On Wed, 26 Sep 2001, Fritz Roth wrote:

> Hi GOfriends,
> 
> So I gathered from response to my last email about redundant GOIDs that 
> there is a rule that when multiple GO IDs are listed for a given attribute, 
> only the first GOID is used in the gene association file.
> 
> Using todays versions of ontologies and gene_association files available 
> from ftp://ftp.geneontology.org/pub/go/, there are still a few GOIDs in SGD 
> and FlyBase that violate this rule.  All MGD GO IDs conformed to the rule.
> 
> Thanks,
> Fritz Roth
> 
> SGD:
> 0008557
> 0003710
> 
> FlyBase:
> 0005372
> 0017122
> 0003710
> 0019006
> 0017167
> 0016940
> 00058924
> 00036763
> 0018999
> 00057622
> 
> NOTE: My script does not discriminate between a) IDs used in the 
> gene_association table that are not found in any ontology file, and b) 
> those IDs that are in the ontology file, but not first in a list of 
> redundant IDs, so some IDs in the Flybase list may fall into the (a) category
> -------------------------------------------------
> 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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