[go] concern about 'tricarboxylic acid cycle intermediate metabolic process' GO:0006100

[Valerie Wood]

I'd be very happy to see it go. I was looking at this last week and 
wondering why lys2 was appearing under carbohydrate metabolism and that 
it came from this term, but i coun't work out what the actual problem was.

I have deleted my annotation already so there are only 2 direct 
annotations remaining

Val


Midori Harris wrote:

> Hi all,
>
> In SF 1894620, I corrected a true path violation for 'TCA cycle' 
> (GO:0006099) that Peter D'Eustachio noticed. That work also brought 
> 'tricarboxylic acid cycle intermediate metabolic process' (GO:0006100) 
> to our attention. It has the same parent -- 'cellular carbohydrate 
> metabolic process' (GO:0044262) -- that caused the TPV for TCA cycle, 
> but has no other parents. Peter and I reached the conclusion that 
> GO:0006100 serves merely as a  grouping term from "metabolism of 
> molecules that make an appearance in the TCA cycle", and that, while 
> not entirely nonsense, having 'cycle intermediates' process terms is a 
> really rich sources of tpv's.
>
> We therefore suggest that the safest course of action is to make 
> GO:0006100 obsolete. Annotations can be transferred to TCA cycle or to 
> one of the children of GO:0006100.
>
> Before I start the procedure to make GO:0006100 obsolete, can anyone 
> recall or think of any reasons to keep the term? If we do, I think it 
> would have to go directly under cellular metabolic process.
>
> https://sourceforge.net/tracker/index.php?func=detail&aid=1894620&group_id=36855&atid=440764 
>
>
> Midori
>
>
>



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