[Ontology-editors] draft has_part announcement

[David Hill]

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
>
>

-- 
David P. Hill, Ph.D.
Bioinformatics Scientist: Ontology Development
Gene Ontology Consortium
The Jackson Laboratory
www.geneontology.org
www.informatics.jax.org
tel:207-288-6430