term: columella

[katica at acoma.Stanford.EDU]

My two cents:

On Fri, 5 Aug 2005, Pankaj Jaiswal wrote:

>
> <http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=columella>
>
> Please correct me if I am wrong.
>
> As I understand it the term  PO:0020130 : central root cap is  a region in 
> the root cap and its synonym "columella cells" is inappropriate. Also I see 
> that a similar term  PO:0020132 : columella root cap cell exists, so the 
> synonym "columella cells" should actually be added to  PO:0020132 : columella 
> root cap cell and removed from PO:0020130 : central root cap.

Central root cap IS columella, hence synonym 'columella cells'; I would 
perhaps remove cells from this synonym. (BTW, that's why the definitions 
in PO and in Esau are the same.)

>
> A renaming of the term PO:0020132 : columella root cap cell to "central root 
> cap cell" will help, thus maintaining consistency with parent term. 
> Additional parent term for  PO:0020132 : columella root cap cell is a must as 
> follows.
>
> PO:0020130 : central root cap
> ---part_of--PO:0020132 : columella root cap cell
>
> For consistency the renaming is suggested for  PO:0020133 : columella root 
> cap initial to "central root cap initial"

This term 'PO:0020132 : columella root cap cell' resides only under tissue 
(meristem) and cell node. When making these nodes, we agreed that terms
from tissue and cell node would not be propagated initially elsewhere in 
the ontology, unless there is specific reason for that (mostly annotation 
requirements). So, unless we have such a reason, this term could stay 
where it is right  now.

New name, 'central root cap cell' is fine, but these cells are called 
'columella root cap cells' in the literature, and I am inclined to keep it 
as such; perhaps adding a synonym 'central root cap cell' would serve the
purpose.


> -----------------------
>
> Just to clarify the usage of word "columella"
>
> My understanding is that the term "columella" is popularly called as : The 
> central part of root cap in which the cells are arranged in longitudinal 
> files (ref: Essau).  We are using the same definition for defining the 
> "central root cap" (syn columella cells) and they are the same structure we 
> are talking about.
>
> However there is a confusion by use of the word "columella" in the term 
> PO:0020014 "columella"  A rod-like element of the sexine/ectexine, either 
> supporting the tectum or a caput.
>
>
> To make it very clear we are talking about root cap columella in one place 
> and pollen wall columella in another can we do the renaming of
>
> PO:0020014 "columella" to "pollen wall columella"

This is unnecessary, in my opinion, since the lineage of the 
term 'columella' as in pollen wall is sufficient to distinguish it from 
columella in the root cap. This is preciselly why the hierarchical 
structure of ontology is useful, i.e., term lineage (parentage) adds up to 
the sum total of information about a term, beside its name and definition.
Otherwise, we would have opted for a flat structure, something like a
dictionary.

Note: this is different from having two terms with same name and same or 
similar definitions. Here, we have two terms (term and a synonym of 
another term) with different definitions, describing very different concepts, 
which makes it legitimate to keep them as they are.


Katica



  > > -Pankaj 
> > >

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