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Quick GO - Problems finding terms

Midori Harris midori at ebi.ac.uk
Tue Sep 11 03:02:31 PDT 2001


Hi Bosse,

We will handle obsolete terms differently in the relational database (they
will be tagged within the db), but in the meantime, we haven't changed
anything about what we do with them.

The second part of Tom's statement is an accurate description of what's
done when we change the meaning of a term: the old term and ID become
obsolete and a new ID is generated, even if the text string is unchanged.
That is, a GO ID is connected to the definition rather than the text
string.

The first part of Tom's statement, to the effect that terms had been
totally removed, applies only to InterPro's internal copy of the GO data.
The terms have not been removed from the GO flat files, or even moved
within the flat files. I belive Tom is checking up on why they weren't
included in the InterPro database.

On Mon, 10 Sep 2001 Bo.Servenius at astrazeneca.com wrote:

> Hi Midori,
> 
> You did not comment on Tom's statement below
> 
> These obsoleted terms - disappearing completely and reappearing in other
> places are really annoying. 
> 
> BTW I think the obsoleted terms should be more clearly marked - e.g with a
> change in term name - add "obsolete" in front of the term. Then it should be
> less risk that you misinterprete a listing of terms from say a clustering of
> function terms. As the situation is now obsoleted function terms are as
> valid belonging to the function tree as correct function term and that I do
> not think is very smart.
> 
> I think that we need some sort of more formalised handling of the terms that
> are to be "obsoleted".
> 
> 
> Yours
> 
> Bosse
> 
> 
> 
> > Well, it appears that these terms have been totally removed from the
> > latest release of the GO (we update daily, I did a manual update this
> > morning to check that this wasn't our data going out of synch), and that
> > the terms have been replaced with identically named (but seemingly
> > better defined) terms with different IDs. Midori - is this correct?
> > 
> > Cheers,
> > 
> > Tom
> > 
> 




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