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

[Alexander Diehl]

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


-- 
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