[Ontology-editors] CC organization question for xps

[Tanya Berardini]

Chiming in REALLY late here...

On Mon, Nov 17, 2008 at 2:51 AM, Midori Harris <midori at ebi.ac.uk> wrote:

> Hi all,
>
> 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.


I can understand this.


> 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


This disturbs me a little bit exactly for the reason you point out below,
the resulting path up to 'developmental process'

"but some users may think it looks odd if they've been accustomed to
thinking of 'development' having a narrower meaning."

I am reluctant to redefine what 'development' means for the broader
community by making this parentage.  Here are some specific children of
'cellular component assembly' that make me hesistate:

'actin cortical patch assembly'
'chromatin assembly'
'macromolecular complex assembly'

There are others as well, but these should serve to illustrate cases where
'% assembly' is not part of a progression from an initial condition to a
later condition.  I really don't think that anyone would consider 'protein
complex assembly' a developmental process even if GO's definition is broad
enough to encompass this term.

>Note that we already have GO:0032989 cellular structure morphogenesis is_a
GO:0009653 anatomical structure morphogenesis.

That parentage makes sense to me and I think it should stay.

What happens if we don't make the link between 'cellular component assembly'
and 'anatomical structure formation'?

It still makes sense to add  cellular component formation as an exact
synonym of cellular component assembly.

I'm not so sure now whether we still would want to merge GO:0016043
(cellular component organization) and GO:0032989 (cellular structure
morphogenesis) and add the relationship GO:0022411 (cellular component
disassembly) is_a GO:0060033 (anatomical structure regression)?

There's my monkey wrench.  Let's discuss.

Tanya


>
> 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.)
>
> GO:0022607 (and GO:0016043, if we decide on an anatomical structure process
> parent for it) will acquire a path back to GO:0032502 developmental process.
> The definition GO uses for developmental process is broad enough to be
> consistent with the new paths, and it would be entirely consistent with our
> thinking about the CC organization terms, but some users may think it looks
> odd if they've been accustomed to thinking of 'development' having a
> narrower meaning. I can live with that, but we should be prepared for
> questions.
>
> Note that we already have GO:0032989 cellular structure morphogenesis is_a
> GO:0009653 anatomical structure morphogenesis.
>
> Shall I go ahead and add GO:0022607 is_a GO:0048646?
>
> m
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-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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