[Ontology-editors] constituent part

[Chris Mungall]

I think we should add a disjoint relation between "cell part" and  
"extracellular region part" (to allow OE to auto-detect other errors  
of this sort)

See:
http://wiki.geneontology.org/index.php/ 
Cellular_component_disjoint_classes

On Jul 8, 2008, at 12:41 PM, Jane Lomax wrote:

> 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?
>>>> _______________________________________________
>>>> Ontology-editors mailing list
>>>> Ontology-editors at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>
>>>
>>> -- 
>>> 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
>>>
>>>
>
>
> -- 
> 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
>
>