[Ontology-editors] constituent part

[Jane Lomax]

Looks like this is the offending relationship:

 / GO:0005576 extracellular region
  po GO:0020008 rhoptry {via is_a extracellular region part}

I can't find anything in the literature to indicate that the rhoptry is 
extracellular (see 
http://www.nature.com/nrmicro/journal/v6/n1/fig_tab/nrmicro1800_F3.html). 
Anyone object if I go ahead and delete this relationship?

Jane



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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>>> Ontology-editors at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>
>>
>> -- 
>> Dr Jane 
>> Lomax                                                                 
>>                                          GO Editorial 
>> Office                                                                
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>> EMBL-EBI                                                                   
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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