New terms in PO

[Pankaj Jaiswal]

Katica Ilic wrote:
> Hi,
> 
> I agree with Leonore and here is one more point to the discussion
> about hypocotyl hook. If the term 'hypocotyl hook' end up being a synonym
> of 'hypocotyl' in PO, (which I think is not right, even with different kinds of synonymy
> currently in use by GO), all the annotations to this term would show up
> under hypocotyl. So, if curators could use term hypocotyl, we wouldn't
> have had their request for this term at the first place.
> 

That's a valid case, but I must say it is growth stage dependent. There 
is no hook  after it straightens, whereas if you have a term for a 
region then it may make sense. such as towards apical end of hypocotyl 
(apical pre-elongation region) and elongated mature base.

I am open to this term.


> Cauline and rosette leaf:
> Felipe, I understand you rationale, and those were the reasons that these
> terms did not make it to the PO in the first round (back in May), but now,
> we are talking about a need to facilitate annotations. Perhaps I was not
> specific enough when I included info about gene annotations in TAIR. Genes
> annotated to the term cauline leaf are not necessarily the same as those
> annotated to rosette leaf (although, four out of five genes are expressed
> in both, cauline and rosette leaves). They would all show up if you query
> term 'leaf', but unless we have the cauline and rosette leaf as separate
> terms, we can never see the annotation to each, nor would we be able to
> ask which genes are expressed in cauline leaves, but not in rosette leaves
> (for instance PPCK1 is expressed in mainly in rosette leaves, while PPCK2
> is expressed in roots and cauline leaves, see Plant, Cell and Environment,
> 2002, 25:115-122). This is the reason it wouldn't work if we make rosette
> leaf a synonym of term leaf, as Pankaj suggested.
> 
> Katica
> 

The rosette annotation can go to the generic leaf and the rest to the 
new simple leaf instance cauline leaf. I was just supporting Leonore's 
statement on having a new term for Cauline.

You will be able to generate a statement show me all the genes that are 
expressed in leaves BUT not in cauline leaves.
or
those in cauline leaves BUTNOT in leaves (rosette leaves). Use of 
rosette leaves will work here because its is there as a synonym.

BTW TAIR also has adult leaf in Arabidopsis. How does the adult leaf 
differ from any of the rosette or cauline leaf.

Pankaj