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Use of non-primary GO IDs in gene association tables

Fritz Roth froth at hms.harvard.edu
Wed Sep 26 14:44:11 PDT 2001


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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