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

[Chris Mungall]

An alternative convention is to think in terms of sentences rather  
than edges, and of the linguistic roles 'subject' and 'object' instead  
of parent/child.

E.g. in the sentence

	[every] T cell has_part [some] T-cell receptor

The subject of the sentence is "T cell" and the object is "T-cell  
receptor"

Of course, 'subject' and 'object' each come with their own baggage.  
But at least this convention is well established in GMOD databases and  
the semantic web world.

Personally I like "referent" and "relatum". This is standard in  
predicate logic. But it sounds a little too formal to catch on.

On Jun 16, 2009, at 1:01 PM, Alexander Diehl wrote:

> I agree with your restatement (hadn't thought deeply about  
> has_part).  We shouldn't let use of the terms 'child' and 'parent',  
> which worked well for the original GO with its is_a and part_of  
> relationships burden our thinking about other relationship types,  
> particularly as the GO is rebuilt with logical definitions based on  
> relationships to other terms both within and external to the GO.
>
>
> Chris Mungall wrote:
>>
>> 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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>>>>> Ontology-editors at geneontology.org
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>>>> _______________________________________________
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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
>>>
>>>
>>
>
>
> -- 
> 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
>
>