[Ontology-editors] haspart documentation (meeting with Chris (fwd))

[Chris Mungall]

On Jun 16, 2009, at 10:05 AM, Alexander Diehl wrote:

> I have to agree with Chris.  Graphical conventions should always be  
> readable in the same direction with term1 (the child) having a  
> relationship to term2 (the parent), so that the combination can be  
> turned directly into an English sentence.
>
> T cell is_a lymphocyte
> T cell --is_a--> lymphocyte
>
> I think the problem here is that the whole idea of child and parent  
> does not apply to non-transitive relations.

I would say "does not apply to many relations, including non- 
transitive relations"

(has_part is transitive)

>  After all, many non-transitive relationships will be between  
> different ontologies:
>
> T cell differentiation has_participant T cell.
> T cell differentiation ---has_participant-->  T cell
>
> T cell has_part T cell receptor
> T cell ---has_part--> T cell receptor
>
> Thanks,
>
> Alex
>
>
> Jennifer Deegan (nee Clark) wrote:
>> Is there a known correct use of parent/child for has_part? It seems  
>> to me that has_part is bound to be a bit tricky, but that if there  
>> is a correct usage then it would be best if we find out what it is  
>> and try to stick with it from day 1.
>>
>> Jen
>>
>> Amelia Ireland wrote:
>>>
>>> On Jun 16, 2009, at 7:08 AM, Chris Mungall wrote:
>>>
>>>>
>>>> Unfortunately, the whole 'parent/child' terminology becomes  
>>>> confusing with has_part
>>>> http://www.ebi.ac.uk/~aji/go/ 
>>>> GO.ontology.relationships.shtml#haspart
>>>>
>>>> If we take 'child' to mean the subject of the assertion, and  
>>>> 'parent' to mean the target/object of the assertion, then in
>>>>    chromosome has_part chromatin
>>>>
>>>> chromosome is the child and chromatin is the parent
>>>>
>>>> This usage is consistent with our graphical metaphors, where we  
>>>> always have child ---> parent
>>>>
>>>> Of course, this conflicts with the intuition we have drummed into  
>>>> people after 10 years, where 'child' is the smaller and 'parent'  
>>>> is the larger.
>>>
>>>
>>> I would argue that your average everyday mortal (e.g. me)  
>>> considers the parent to be the broader term (closer to the root  
>>> node) and the child to be the more specific term. If I've used the  
>>> terms 'child' and 'parent' in the opposite way somewhere, it's  
>>> accidental, and due to a copy/paste error!
>>>
>>> Perhaps I'll add something at the top about the nomenclature  
>>> conventions used in these docs so it's not so confusing.
>>>
>>> -- 
>>> Amelia Ireland
>>> GO Editorial Office
>>> http://www.berkeleybop.org || http://www.ebi.ac.uk
>>> BBOP Plant Project: http://bbopgarden.blogspot.com
>>>
>>>
>>>
>>>
>>>
>>>
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>
>
> -- 
> Alexander D. Diehl, Ph.D.
> Senior Scientific Curator
> Mouse Genome Informatics
> The Jackson Laboratory
> 600 Main Street
> Bar Harbor, ME  04609
>
> email:  adiehl at informatics.jax.org
> work:  +1 (207) 288-6427
> fax:  +1 (207) 288-6131
>
>