term: columella

[katica at acoma.Stanford.EDU]

What we have here is a term and a non-related synonym with the same 
name (assuming that 'columella cells' would be changed to 
'columella'). So, it's a simple question: Is it confusing for our users
to have 'columella' as synonym of 'central root cap' and also as a term 
(someplace else in the ontology) with its synonym 'sexine 1'.

These four terms came out in AmiGO when searching for 'columella':

PO Term				Synonyms
central root cap		columella cells
columella			sexine 1
columella root cap cell		NONE
columella root cap initial	NONE

I can't speak for ontology users, but my guess is that it's more or less 
obvious for an average user. It would be useful and interesting to hear 
from ontology users on this topic.

Katica




On Mon, 8 Aug 2005, Pankaj Jaiswal wrote:

> Peter Stevens wrote:
>
>> Seems OK to mre, but I would suggest not having "pollen wall coluella" as 
>> the name of the term: if we are in the pollen wall part of the ontology, 
>> "columella" alone will do the trick if the root "columella" has been 
>> obsoleted.  Applying any principle of qualifying terms based on 
>
> The root columella is not obsolete, we have renamed the term to PO:0020130 : 
> central root cap.
>
>
>> the particular part of the plant where they are to be found will ultimately 
>> lead to wholesale "renaming" of terms. However, there is also a term 
>> "columella" used in fruits that applies to the central axis that persists 
>> after the rest of the fruit wall has separated and/or fallen off.  If we 
>> were to keep this term, then qualification might be needed, but again, one 
>> would be be in a totally different part of the ontology - qualification 
>> would then be driven by the needs of our particular controlled 
>> vocabulary....
>> 
>
> The example given by you is an excellent one considering the ambiguous usage 
> of the anatomical terms in the classical literature. Therefore to me, it is 
> more or less suggesting us to create the terms with their anatomical location 
> attributes (pointing to the composite terms). This is so because even though 
> the definition and the parent-child relationships in an ontology tree, make a 
> term unique if the same term name is used, it is often confusing for the 
> users if they are looking at the term only and not at the definition or the 
> term's lineage. Often the stand alone terms are easy to suggest what they are 
> based on their uniqueness, but not always as in the case of columella.
>
>
>
>> P.
>> 
>> 
>>> 
>>> <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.
>>> 
>>> 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"
>>> 
>>> -----------------------
>>> 
>>> 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"
>>> 
>>> -Pankaj
>> 
>> 
>> 
>
>

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