terms for fruit development stages

[katica at acoma.stanford.edu]

I annotate Arabidopsis mutants to PO terms as well as to GO terms (lately 
have been using PATO too). Naama's initial request for 
'fertilization' sounded like a process term to me, in which case GO
would likely have appropriate terms.

For this very reason we don't have fertilization as a stage in PO.

As for the other two requests, I'll include them as items for the next 
conf call.

Katica

On Mon, 3 Apr 2006, Pankaj Jaiswal wrote:

> I am not an expert on this, but I presume Naama is trying to annotate her 
> mutants suggesting the phenotype affects/observed_at this stage. Now the 
> problem is this stage is also a process term in GO. Which is fine as long as 
> we call it as a stage. We do have terms like these in plant part 
> developmental stages like leaf development etc. that overlap with GO 
> processes. In such cases we appended the term with a X-stage.
>
> Pankaj
>
> katica at acoma.stanford.edu wrote:
>
>> Peter and Naama,
>> 
>> I see. For the events that precede double fertilization, there are several 
>> terms in GO, I pulled out some of them; Naama please take a look in GO 
>> process ontology for more:
>> 
>> pollen germination  GO:0009846
>> Def: The physiological and developmental changes that occur in a 
>> heterosporous plant pollen grain, beginning with hydration and terminating 
>> with the emergence of the pollen tube through the aperture.
>> 
>> pollen tube guidance  GO:0010183
>> Def: The process by which the growth of pollen tube is directed towards the 
>> female gametophyte.
>> 
>> pollen tube growth  GO:0009860
>> Growth of pollen via tip extension of the intine wall.
>> 
>> Katica
>> 
>> On Mon, 3 Apr 2006, Peter Stevens wrote:
>> 
>>> Nama is really talking about what goies on before the actual act of double 
>>> fertilisation, or at least double fertilisation is at the very end of his 
>>> whole process of fertlisation.
>>> 
>>> P.
>>> 
>>> 
>>>> Hi Naama,
>>>> Double fertilization is already in GO:
>>>> 
>>>> "double fertilization (sensu Magnoliophyta)'
>>>> GO:0009567
>>>> 
>>>> Can you use this term? At POC, we agreed to avoid duplication of terms
>>>> with Gene Ontology.
>>>> 
>>>> Katica
>>>> 
>>>> On Mon, 3 Apr 2006, Naama Menda wrote:
>>>> 
>>>>  > I need the following terms for annotating tomato genes expressed 
>>>> during
>>>> 
>>>>>  different fruit development stages:
>>>>> 
>>>>>  -fertilization: The stage of successful pollen germination, 
>>>>> penetration, and
>>>>>  growth of the pollen tube in the stylar tissue towards the ovule and 
>>>>> into the
>>>>>  embryo sac for fusion with the egg cell. Dbxref PMID:12271039
>>>>> 
>>>>>  -fruit cell division: The initial stage of fruit development triggered 
>>>>> in the
>>>>>  fruit primordia. Dbxref PMID:12271039
>>>>> 
>>>>>  -fruit cell expansion: The stage of increase in cell volume, 
>>>>> contributing
>>>>>  mostly to fruit growth. Dbxref PMID:12271039
>>>>> 
>>>>> 
>>>>>  Thanks
>>>>>  -Naama Menda
>>>>> 
>>>> 
>>>> -- 
>>>> 
>>>> -------------------------------------------------------------------------- 
>>>> Katica Ilic                             katica at acoma.stanford.edu
>>>> The Arabidopsis Information Resource    Tel: (650) 325-1521 ext. 253
>>>> Carnegie Institution of Washington      FAX: (650) 325-6857
>>>> Department of Plant Biology             URL: 
>>>> <http://arabidopsis.org/>http://arabidopsis.org/
>>>> 260 Panama St.
>>>> Stanford, CA 94305
>>>> U.S.A.
>
>

-- 
--------------------------------------------------------------------------
Katica Ilic             		katica at acoma.stanford.edu
The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington 	FAX: (650) 325-6857
Department of Plant Biology 		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
U.S.A.
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