[Ontology-editors] draft has_part announcement

[Midori Harris]

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)]