[Ontology-editors] ferrichrome question (SF 2528716)

[Gwinn Giglio, Michelle]

Hi,

Yes, I see what you mean.  I guess then that peptide modification could not
have macromolecule as a parent, since all peptides are not part of
macromolecules.  Depending on how we define macromolecule.

I'm hampered here by my lack of knowledge on the synthesis of these
molecules.  But, I'm a little concerned with the children terms that
separate peptide formation and peptide modification.  It seems to me that
peptide formation is what this synthesis is all about.  I'm not clear on how
that term is really different than its parent - it seems that having that
child term is splitting out one function of the process.

Maybe that term exists because of the need for the modfication term.  If
sometimes these are modified and sometimes they are not.  But if they are
always modifed, then again it seems like it is turning a function into a
process - taking one of the functional steps in a pathway and making a
process term for it.

Or maybe I'm just very confused.

Michelle



On 1/26/09 11:41 AM, "Midori Harris" <midori at ebi.ac.uk> wrote:

> Thanks for the quick response!
> 
> I think I see where the macromolecule parent came from -- it's because of
> the peptide modification ancestor. The term name could be reworded
> "peptide modification involved in ferrichrome biosynthetic process", but
> if that would still be too weird, we can remove the parent. It would then
> be odd to have a term with "peptide modification" in the name that doesn't
> have a path back to the generic "peptide modification" parent, though.
> 
> Which is the lesser problem?
> (adding the ont-eds list because of the consistency issue ...)
> 
> m
> 
> On Mon, 26 Jan 2009, Gwinn Giglio, Michelle wrote:
> 
>> 
>> Hi,
>> 
>> The current structure is definitely strange.  See also that the sibling term
>> "ferrichrome biosynthesis, peptide formation" does not have the
>> macromolecule parent.  I would be inclined to take away the  macromolecule
>> parent.  It does not fit with my understanding of macromolecule.
>> 
>> Michelle
>> 
>> 
>> 
>> 
>> 
>> On 1/26/09 11:13 AM, "Midori Harris" <midori at ebi.ac.uk> wrote:
>> 
>>> Hi Michelle,
>>> 
>>> Val has pointed out that it's a bit confusing to have one path from
>>> 'ferrichrome biosynthetic process, peptide modification' (GO:0031200) lead
>>> back to macromolecule metabolic process, whereas another path doesn't.
>>> Should we make any changes?
>>> 
>>> Let me know if I can explain better, or help.
>>> 
>>> https://sourceforge.net/tracker/index.php?func=detail&aid=2528716&group_id=3
>>> 68
>>> 55&atid=440764
>>> 
>>> Thanks,
>>> midori
>>