fruit section

[Pankaj Jaiswal]

Elizabeth Kellogg wrote:

> Hi Pankaj -
>    The problem is that not all legumes dehisce, and the ones that do  
> dehisce do not all do it in the same way - some dehisce along one  
> suture, some along both, and some dehisce between the seeds.  The term  
> "legume" can only be defined strictly as "the fruit of a member of  
> Leguminosae."   That's why it ends up as an instance only of fruit and  
> not of "seed as dispersal unit."

This is fine. I did not know about the situation earlier. Can we revise 
the definition we have now:
The fruit of Fabaceae, formed from one carpel and either dehiscent along 
both sides, explosively so or not, or indehiscent, winged or not, 
splitting transversely or not.

>   The TPR violation comes from the attempt to include a time axis  
> (development) in a structural ontology, along the lines that we were  
> discussing last week.   The relationships are not intrinsically  
> hierarchical.  We could create "floret gynoecium", but following the  
> same logic we might also have to create a separate term for every sort  
> of gynoecium that developed into a different kind of fruit.   But I  
> don't quite understand the example you've given below.  Aren't there  
> other instances of fruit, including indehiscent ones?  I think the TPR  
> violation in the example below comes from reading down the hierarchy.   
> Presumably if you included indehiscent fruits then you could trace a  
> true path from caryopsis up to floret.  (I think....)

I guess in this case we may need to pull back the develops from 
relationship (fruit-gynoecium). Because reading down the hierarchy also 
matters when we start associating the terms to genes/phenotypes. The 
asssociations keep adding from  bottom-up. e.g. genes expressed in 
anthers are also considered to be expressed in stamen as well as its 
parent terms flower and floret. All the associations of a child term are 
carried over to the parent term by default in addition to any direct 
associations that teh parent might have. So anything associated with 
silique will also show up with floret and its parent spikelet, which 
should not happen.

> Toby
> 
> On May 10, 2004, at 1:25 PM, Pankaj Jaiswal wrote:
> 
>>
>> Hi,
>>
>> I have some comments on fruit section
>>
>> -term "legume" is currently  a direct instance of fruit. Do you think  
>> it should be placed as an instance of term "seed as dispersal unit",  
>> which is an instance of dehiscent fruit.
>> -do we need all the instances of (sort of attributes) of capsule, 
>> e.g.  loculicidal, septicidal etc. I know the exclusion of 
>> "septifragal"  will be difficult because of the following comment. Is 
>> there a way  out?
>> -people may like to see "slilique" as a primary term compared to a  
>> synonym for "septifragal"
>> -a possible TPR violation..
>>     generic term gynoecium appears under floret and this may cause 
>> TPR  violation because not all the fruit types develop from  "floret  
>> gynoecium" (newly coined term). It's only the "caryopsis" which  
>> develops from gynoecium in the floret. We need a resolution on this.
>>
>> may be we need to pull back the relationship
>> fruit  develops from gynoecium
>>
>> One such example is slilique appearing under floret..
>>
>> http://brie.cshl.org:8080/amigo/go.cgi? 
>> action=replace_tree&search_constraint=terms&query=PO:0020072
>>
>>      <inflorescence branch ; PO:0009081 ; synonym:coflorescence
>>       %spikelet ; PO:0009051
>>        <floret ; PO:0009082
>>         <gynoecium ; PO:0009062 ; synonym:pistil < flower ; 
>> PO:0009046  % reproductive structures ; PO:0009083
>>          ~fruit ; PO:0009001 % mature dispersal unit ; PO:0009091
>>           %dehiscent fruit ; PO:0020064
>>            %seed as dispersal unit ; PO:0020081
>>             %capsule ; PO:0020067
>>              %septifragal ; PO:0020072 ; synonym:silicula ;  
>> synonym:siliqua ; synonym:silique
>>
>>
> Elizabeth A. Kellogg
> E. Desmond Lee and Family Professor of Botanical Studies
> Department of Biology
> University of Missouri-St. Louis
> St. Louis, MO 63121
> Tel: 314-516-6217
> FAX: 314-516-6233
> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ home.html
> 
> 

-- 
************************
Pankaj Jaiswal, PhD
G15-Bradfiled Hall
Dept. of Plant Breeding
Cornell University
Ithaca, NY-14853, USA

Tel: +1-607-255-3103
      +1-607-255-4109
Fax: +1-607-255-6683
http://www.gramene.org
************************