Re: [Obo-anatomy] how to classify tricky plant parts - ovaries

[Alan R. <ala...@gm...>]

On Monday, May 21, 2012, Walls, Ramona wrote:

>  One thing I forgot to say in my comment below: If we were to create two
> separate terms for ovary (one for single carpels and one for fused
> carpels), we would have to create two sets of all of the structures that
> have a part_of relation to ovary.
>

Why?

We run into this problem all the time, and we aren't happy with any of the
> current solutions. There really is no difference between and ovule that is
> part of an ovary in a single versus an ovule that is part of an ovary in a
> group of fused carpels.
>
>  Ramona
>
>   From: Ramona Walls <rw...@ny... <javascript:_e({}, 'cvml',
> 'rw...@ny...');>>
> Date: Mon, 21 May 2012 09:29:38 -0400
> To: Chris Mungall <cjm...@lb... <javascript:_e({}, 'cvml',
> 'cjm...@lb...');>>, Alan Ruttenberg <ala...@gm...<javascript:_e({}, 'cvml', 'ala...@gm...');>
> >
> Cc: "obo...@li... <javascript:_e({}, 'cvml',
> 'obo...@li...');>" <obo...@li...<javascript:_e({}, 'cvml', 'obo...@li...');>
> >
> Subject: Re: [Obo-anatomy] how to classify tricky plant parts - ovaries
>
>   Thank you for all the very helpful feedback. I'm sorry I couldn't
> participate in this discussion while it was going on. I have copied parts
> of several emails into one, since the thread diverged a bit at one point.
> My responses in line are in blue.
>
>  Ramona
>
>
>  From mejino@u.washington.edu:
>
>  It seems to me that the ovary is just part of a bigger structure,
> gynoecium (pistil)?. Would you consider gynoecium an organ? If so, ovary is
> a cardinal organ part, regardless of whether it is a single carpel
> (monocarpous ovary) or multiple connate carpels (syncarpous ovary).
>
>
>  RW: We do not consider an gynoecium an organ. It is a collection of
> organs – all of the carpels in a flower. Sometimes it has one carpel, and
> sometimes it has many. Sometimes they are fused, sometimes they are free,
> sometimes they are partially fused. Sometimes they start out free, and then
> become fused later. Only when the carpels are free is it correct to call an
> ovary a cardinal organ part.
>
>
>    From Alan:
>
>  Structural definitions are not the only way anatomy is classified,
> others being (at least) developmental and functional. I would think that in
> this case you would have two structural terms for ovary, distinguishing
> them appropriately logically and terminologically, and then have a
> functional grouping for the ovary class you are talking about. I believe
> this is the sort of thing UBERON does.
>
>   RW: I don't know how I would create such a grouping using a logical
> definition. We do not want to add functional relations as part of the main
> PO (although, at some future point, an additional file that adds functional
> relations on top of the PO seems like a good idea), and in any case, I
> think it is their structure and position that unite the two types of
> ovaries, as much as their function. I may be able to come up with a logical
> definition for a class that includes both type of ovaries, I still don't
> know what the parent term for that class would be (see below).
>
>    From Chris:
>
>    Correct - and GO and various other ontologies.
>
>  I don't know enough about plants to say whether multiple classes are
> biological justified here, or whether this is just an abstruse workaround
> to fit in with some upper ontology classes. On the surface it would seem
> like this is a big structural difference, warranting two separate
> subclasses.
>
>
>  RW: Botanists don't generally think of them as two separate classes, but
> creating two structures would be fine (one is a cardinal organ part and one
> is a collective organ part structure). However, we still want one class
> that includes them both, and that is where we are stuck. How should that
> parent class, that includes both cardinal organ parts and collective organ
> part structures, be classified? Right now we are stuck with making it a
> plant structure (very general term), but the subclasses of plant structure
> are getting to be too numerous, and we would like to have another level of
> classification. That is why I thought of CARO:multi-tusse structure or
> CARO:organism subdivision.
>
>