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

[Tanya Berardini]

I can move our annotation to the TCA term.

Tanya

On 2/21/08, Tanya Berardini <tberardi at acoma.stanford.edu> wrote:
>
> I'll have a look at the one annotation that TAIR has to this term.
>
> Tanya
>
> On 2/21/08, Valerie Wood <val at sanger.ac.uk> wrote:
> >
> >
> >
> > 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
> > >
> > >
> > >
> >
> >
> >
> >
> > --
> >   The Wellcome Trust Sanger Institute is operated by Genome Research
> >   Limited, a charity registered in England with number 1021457 and a
> >   company registered in England with number 2742969, whose registered
> >   office is 215 Euston Road, London, NW1 2BE.
> >
>
>
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