[Ontology-editors] ferrichrome question (SF 2528716)

[Midori Harris]

Hi,

I'm confused too ... I looked yesterday, and this is what I found on the 
history of the existing terms:

https://sourceforge.net/tracker/index.php?func=detail&aid=1117949&group_id=36855&atid=440764

So Val, the parentage you queried was your idea a while back!

If we decide we don't need the peptide modification and peptide formation 
terms, we could merge them into the corresponding parent terms (for 
siderophore biosynthetic process and quite a few of its children), and 
remove the peptide-related parentage from the resulting terms. It might be 
a bit incomplete for the peptide siderophores, but whether that's a big 
loss isn't for me to decide. There are only two annotations to any of 
the terms, both from S. pombe. What do you think?

m

On Mon, 26 Jan 2009, Gwinn Giglio, Michelle wrote:

>
>
> 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
>>>
>