[Ontology-editors] CC organization question for xps

[David Hill]

Comments follow.
> I have a suggestion and question about the CC organization terms that 
> are relevant to XPs ...
>
> Several of us agreed recently that all cellular components are 
> anatomical structures. For the xp set I'm looking at -- 
> biological_process_xp_cellular_component.* -- I can put in more 
> specific genus terms for several xp defs if I add the relationship:
>
> GO:0022607 cellular component assembly is_a GO:0048646 anatomical 
> structure formation
Would it make sense then to have an exact synonym of cellular component 
formation as an exact synonym of cellular component assembly?
>
> It might also be good (though less pressing for my xps) to add a 
> parent in the anatomical structure branch of BP for GO:0016043 
> cellular component organization. I'm not sure whether GO:0048532 
> anatomical structure arrangement exactly fits the bill, though. The 
> definitions don't quite match up, in that GO:0048532 is restricted to 
> "the configuration of the constituent parts of an anatomical 
> structure" and so covers only the "arrangement of constituent parts" 
> part of the GO:0016043 def, not the formation or disassembly. (I also 
> don't quite understand how GO:0048532 can have 'structural 
> organization' as an exact synonym when the more restricted phrase 
> 'anatomical structure organization' is a broad synonym.)
The anatomical terms follow the morphogenesis paradigm. Morphogenesis 
has 3 parts, formation, organization and regression. It seems that these 
would be exactly parallel with assembly, arrangement and disassembly. I 
really would prefer not to rearrange the way the anatomical structure 
morphogenesis terms are organized since Tanya and I put a LOT of thought 
into this. I think GO:0022607 is_a GO:0048646, GO:0016043 and GO:0032989 
might be synonymous and redefined to be parallel with morphogeneis, 
GO:0022411is_a GO:0060033. There is currently no term that would be a CC 
counterpart of GO:0016043, anatomical structure arrangement. Perhaps we 
need to make a new term cellular component arrangement. Note also that 
the defs will need to change a bit since the formation, arrangement, and 
dissassembly would all be a part of morphogenesis.

David