[Ontology-editors] draft has_part announcement

[David Hill]

looks good too.

David

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