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

[Tanya Berardini]

BTW, I meant to agree with Chris on this suggestion:

>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

Tanya

On Tue, Jun 16, 2009 at 7:08 AM, Chris Mungall <cjm at berkeleybop.org> wrote:

>
> 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<http://www.ebi.ac.uk/%7Eaji/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<http://www.ebi.ac.uk/%7Eaji/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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-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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