[Ontology-editors] constituent part

[Midori Harris]

(er, don't understand why GO has that relatoinship; I know why I was 
reading up on 'em!)

On Tue, 8 Jul 2008, Midori Harris wrote:

> 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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>