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

[Chris Mungall]

On Jun 15, 2009, at 3:27 PM, Amelia Ireland wrote:

>
> On Jun 12, 2009, at 2:50 AM, Midori Harris wrote:
>
>> Hi Amelia,
>>
>> If you read the minutes from yesterday carefully, you'll notice  
>> that we volunteered you to write documentation for the has_part  
>> relationship. because Chris told us you had started on it, but put  
>> it on hold when the F-P link team opted for part_of. Now that we've  
>> decide to revive has_part and get it into CC (and BP not too long  
>> after), the documentation is percolating back up the priority heap.
>>
>> Once the documentation is up, we'll announce it on GO Friends and  
>> I'll get on with the test case.
>
>
> http://www.ebi.ac.uk/~aji/go/GO.ontology.relationships.shtml
>
> Questions:
>
> - are those examples OK?
>
> - should I make more of the difference between "has part" and "part  
> of", and that one is from the perspective of the child, whereas the  
> other is from the perspective of the parent?

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.

More specific comments later.

A general suggestion:

it may be a good idea to split the documentation in line with the  
public file split. We would have documentation for the 'standard' GO,  
with no mention of has_part, and additional documentation for GO_ext

>
>
> - have any colours been thought of for the "has part" link?
>
> - in the has-part diagrams, I tried to make a visual difference  
> between the "ALL x ... y" and "SOME x ... y" rules. Does it make it  
> any clearer, or should I just redo those diagrams in the standard  
> style?
>
> Cheers,
> Amelia.
>
> --
> 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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