[Ontology-editors] draft has_part announcement

[Jane Lomax]

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
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