Redundant GO IDs... can we try to use only (the first) one of them?

[Fritz Roth]

Hi All,

As you probably know, there are occasionally multiple GO IDs for a given 
attribute description in a given ontology file.
Example:     %single-stranded RNA binding ; GO:0003727, GO:0003728

It would be convenient to make the assumption that only the GOID listed 
first is actually used anywhere in any gene association table.  This 
assumption actually holds true for the SGD and MGD association tables 
except for one attribute:
      %transcriptional activator ; GO:0016563, GO:0003710 ; 
synonym:transcription activating factor

GO:0003710 is used many times in each gene association table, while 
redundant GOID GO:0016563 is used not at all in SGD, once in MGD and once 
in Flybase.

Perhaps we could switch the order of GO:0016563, GO:0003710 in the ontology 
file and switch use of GO:0016563 in the association tables to GO:0003710 
in the single case it is used in MGD and in Flybase?

Better, maybe we could even eliminate redundant GOIDs altogether and keep a 
lookup table of deprecated IDs elsewhere?

GO:0003710 is the only ID with this problem (redundant GOID where an ID not 
listed first is used in an association table) in SGD and MGD gene 
association tables, and there are just a few more in Flybase:
GO:0017104
GO:0008032
GO:0003710
GO:0016940
GO:0008357

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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