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Problems with gene association files

Gabriel Berriz gberriz at hms.harvard.edu
Tue Jul 2 11:26:00 PDT 2002


Hi, Karen.

>Most of the time, it is fine to map a synonymous GOid to the primary, but 
>I believe there are still instances where a primary GOid was split into 
>two GO terms, each with a new GOid and the original (now secondary) GOid 
>was listed as a synonym for two primary GOids.

Good to know.  I did a quick check of the current ontology files, and found 
only one remaining instance of such splitting (in process.ontology, 0006815 
splits into 0006813 and 0006814).  Our script would have erroneously 
translated 0006815 to either 0006813 or 0006814, but it appears that, at 
least recently, 0006815 is not used in any association, so the erroneous 
translation is never required.  Assuming the script I used to check for 
splits didn't miss any, this suggests that, as long as no more splits like 
this occur, and curators continue to stay clear from 0006815, automatically 
replacing synonymous GOids with the primary should be OK.

>We could probably modify the script to not output associations to 
>synonymous or obsolete IDs while curators are deciding on the replacements.

I think this would be great for obsolete IDs.  For synonymous ones, I would 
vote for automated replacement.

Thanks for shedding light on these questions.

G.


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