[Ontology-editors] draft has_part announcement

[Jane Lomax]

Oh right - I didn't read it properly - it says we can't make *any* 
inference in these cases. I think that's fine then. If we change our 
minds in the future we can always change it.

What do you mean about 'indirectly regulates', David? Do you mean:

A -regulates-> B -regulates-> C

then

A -indirectly regulates-> C

?

Jane

David Hill wrote:
> I think the documentation is fine for now even with the ??? 
> relationships. This basically means that we don't know yet and we are 
> taking the conservative approach. Do you think it would be worthwhile 
> to indicate this? I think we could either go with 'regulates' or 
> 'indirectly regulates'. I kind of like the indirectly because it gives 
> you an idea that you are regulating a regulatory process, but I fear 
> it will cause more confusion.
>
> David
>
> Jane Lomax wrote:
>> Looks fine. I reckon a date of 2 weeks from when the announcement 
>> goes out.
>>
>> We'll have the link to the has_part docs when Amelia's documentation 
>> is released - sounds like it's pretty much ready to go except for a 
>> couple of bits to do with the transitivity of regulates over other 
>> relations which aren't straightforward.
>>
>> Can we comment these bits out so the documentation can be released 
>> now, and fix them when we've made a decision?
>>
>> Jane
>>
>>
>> Midori Harris wrote:
>>> This is a draft message to the GO friends list about adding has_part 
>>> links to the go_ext file. Let me know if anything is wrong or 
>>> missing, or just could stand some editing.
>>>
>>> Things I know are still to do:
>>> - fill in the actual date; have we decided?
>>> - fill in the documentation link
>>>
>>> thanks,
>>> m
>>>
>>> subject:
>>> Announcement: Introduction of has_part relationship in extended GO 
>>> ([date])
>>>
>>> body:
>>> Dear GO Friends,
>>>
>>> We are pleased to announce that we are about to introduce a new 
>>> relationship type, has_part, into the "extended" version of GO 
>>> (ontology/obo_format_1_2/gene_ontology_ext.obo). The target date for 
>>> this addition is [date].
>>>
>>> This addition may have considerable impact on your tools and 
>>> analyses because:
>>>
>>>  1. Loading scripts that use gene_ontology_ext.obo will need to be 
>>> modified to take the has_part links into account by [date].
>>>  2. GO analysis tools that use gene_ontology_ext.obo will need to be 
>>> modified to take the has_part links into account by [date].
>>>  3. The meaning of has_part has important implications for the 
>>> propagation of gene product annotations over relationships in the 
>>> ontology.
>>>  4. There are important display considerations for graphs or 
>>> denormalized trees that include has_part links.
>>>  5. In some cases, the extended GO file will capture more 
>>> information than the "standard" files.
>>>
>>> Has_part links will be added first in the Cellular Component (CC) 
>>> ontology, and later into the Biological Process (BP) ontology.
>>>
>>> The advantage of using has_part in CC and BP is that it will allow 
>>> us to reduce the number of artificial compositional terms that we 
>>> have previously used to avoid introducing erroneous paths in the 
>>> ontology. The graphs will also become somewhat less entangled.
>>>
>>> The has_part relation is documented at:
>>>
>>> [linky]
>>>
>>> Please let us know if you have questions or comments about this plan.
>>>
>>> On behalf of the GO Consortium,
>>> [name(s)]
>>>
>>> _______________________________________________
>>> Ontology-editors mailing list
>>> Ontology-editors at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>
>>
>


-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
f: +44 1223 494468