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Problems with gene association files

Jane Lomax jane at ebi.ac.uk
Wed Jul 3 05:29:42 PDT 2002


Gabriel and Karen,

I fixed all the splits that both retained the old term id as a synonym 
quite recently (moved id to comments field), but obviously I missed one! 
I will fix that last one.  

Splits are *definitely* not handled this way any more, so shouldn't be a 
problem,

cheers

Jane

On Tue, 2 Jul 2002, Gabriel Berriz wrote:

> 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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