[Ontology-editors] constituent part

[Midori Harris]

Rhoptry is_a extracellular organelle ... but I've just been reading about 
them, and i don't understand why.

m

On Tue, 8 Jul 2008, Chris Mungall wrote:

>
> Actually if constituent has no special meaning then the reasoner is correct 
> (the links are not asserted & the reasoner is inferring the links)
>
> / GO:0005576 extracellular region
> po GO:0020008 rhoptry {via is_a extracellular region part}
> / GO:0005623 cell
> po GO:0045177 apical part of cell {via is_a cell part}
>  po GO:0020007 apical complex
>   po GO:0020008 rhoptry
>
>
> On Jul 8, 2008, at 11:48 AM, Jane Lomax wrote:
>
>> Chris - I don't think 'constituent part' has any special meaning in these 
>> defs - we could drop it. The reasoner is right to throw up those "rhoptry 
>> lumen" relationships - they are dodgy, how can it be both a cell part and 
>> extracellular?
>> 
>> Jane
>> 
>> Chris Mungall wrote:
>>> We use the phrase "constituent part" in (almost) all the "X part" terms; 
>>> e.g.:
>>> 
>>> axoneme part [DEF: "Any constituent part of an axoneme, the bundle of 
>>> microtubules and associated proteins that forms the core of cilia and 
>>> flagella in eukaryotic cells and is responsible for their movements."]
>>> 
>>> What exactly does "constituent" mean here?
>>> 
>>> I recall being part of the discussion that lead to this, but can't find 
>>> the relevant emails. Did we just import this term from the FMA? It seems 
>>> to have a specific meaning in anatomy. I can't really find a solid 
>>> definition in the FMA papers.
>>> 
>>> I don't see anything in the component docs either.
>>> 
>>> I think we should either document this or drop it
>>> 
>>> Here's why I'm interested - I define X part generically as a cellular 
>>> component that is part_of X.
>>> 
>>> This means the reasoner throws up:
>>>
>>>    "rhoptry lumen" [GO:0034591] is_a "extracellular region part" 
>>> [GO:0044421]
>>>    "rhoptry lumen" [GO:0034591] is_a "cell part" [GO:0044464]
>>> 
>>> Is there something subtle in the "constituent" qualifier that is missing 
>>> from my xp definition, that simultaneously excludes the above links?
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>> 
>> 
>> -- 
>> Dr Jane Lomax 
>> GO Editorial Office 
>> EMBL-EBI 
>> Wellcome Trust Genome Campus 
>> Hinxton 
>> Cambridgeshire, UK 
>> CB10 1SD 
>> p: +44 1223 492516 
>> f: +44 1223 494468
>> 
>> 
>
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