fruit section

Mon May 10 16:00:30 EDT 2004

Peter - That's a good & strong argument. But I'm wondering if we're not
'throwing the baby out with the bathwater' - this fruit area is very
vexing! Another point for discussion at the May meeting.

- Leszek

> -----Original Message-----
> From: owner-po-dev at brie4.cshl.org 
> [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Peter Stevens
> Sent: Monday, May 10, 2004 1:16 PM
> To: po-dev at plantontology.org
> Subject: Re: fruit section
> 
> 
> >Looking to the future - all taxa in which there is only a single
> >carpel will now need to have fruits with distinct names - e.g. the 
> >nutmeg family (Myristicaceae). No taxon that has several separate 
> >carpels can have a legume fruit, even if the individual fruits are 
> >indistinguishable from a legume as defined below.  Findings aBout 
> >legumes will not easily be generalisable, since nothing else has 
> >them.
> 
> 
> Thus I would strongly recommend against using the term legume as 
> defined below (i.e. the revised definition) - it simply means "fruit 
> of Fabaceae".  If there was a legume s. str. - e.g. "fruit of a 
> single carpel dehiscing explosively down both sutures/sides" that 
> might be OK. I have given up teaching "legume" (or 
> silique/silicle/silicula for that matter).
> 
> Peter S.
> 
> 
> 
> >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/Kel
logg/ 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
>************************