[Ontology-editors] CC organization question for xps
Jennifer Deegan (nee Clark)
jdeegan at ebi.ac.uk
Wed Nov 19 01:46:11 PST 2008
That looks good to me.
Jen
Tanya Berardini wrote:
> Hello everyone!
>
> After discussing with David this morning, and him dissuading me from
> proposing that not ALL cellular components are anatomical structures
> (fuggedabout FMA), I think I get what he's proposed.
>
> Let me try to restate so that I'm sure I've understood him correctly. We
> do NOT make the link between 'cellular component assembly' and
> 'anatomical structure formation' but instead, we create some new terms
> (the ones below containing the string 'involved in morphogenesis') that
> allow us to link up only those children of 'cellular component
> organization' that should have ties to 'developmental process.'
>
> Now:
>
> cellular process
> --[i]cellular component organization
> ----[i]cellular component assembly
> ----[i]cellular component disassembly
> ----[i]cellular component maintenance
> ----[i]cellular structure morphogenesis
>
> developmental process
> --[i]cellular developmental process
> ----[i]cellular structure morphogenesis
>
> developmental process
> --{several steps}anatomical structure morphogenesis
> ----[i]cellular structure morphogenesis
>
> Future:
>
> cellular process
> --[i]cellular component organization
> ----[i]cellular component assembly
> ------[i]cellular component assembly involved in morphogenesis (GO:new)
> ----[i]cellular component disassembly
> ------[i]cellular component disassembly involved in morphogenesis (GO:new)
> ----[i]cellular component maintenance
> ------[i]cellular component maintenance involved in morphogenesis (GO:new)
> ----[i]cellular component morphogenesis (RENAMED FROM: cellular
> structure morphogenesis)
> ------[p]cellular component assembly involved in morphogenesis (GO:new)
> ------[p]cellular component disassembly involved in morphogenesis (GO:new)
> ------[p]cellular component maintenance involved in morphogenesis (GO:new)
>
> developmental process
> --[i]cellular developmental process
> ----[i]cellular component morphogenesis (RENAMED FROM: cellular
> structure morphogenesis)
>
> developmental process
> --{several steps}anatomical structure morphogenesis
> ----[i]cellular component morphogenesis (RENAMED FROM: cellular
> structure morphogenesis)
> ------[p]cellular component assembly involved in morphogenesis (GO:new)
> ------[p]cellular component disassembly involved in morphogenesis (GO:new)
> ------[p]cellular component maintenance involved in morphogenesis (GO:new)
> ----[i]anatomical structure formation
> ------[i]cellular component assembly involved in morphogenesis (GO:new)
> ----[i]anatomical structure regression
> ------[i]cellular component disassembly involved in morphogenesis (GO:new)
>
>
> How does that grab you?
>
> Tanya
>
>
>
>
> On Tue, Nov 18, 2008 at 6:11 AM, David Hill <dph at informatics.jax.org
> <mailto:dph at informatics.jax.org>> wrote:
>
> We could change the existing terms to be for example 'anatomical
> structure formation involved in morphogenesis'. Can anyone think of
> a non-cellular component that would not fall under this category? If
> not, then the cellular component terms can live outside this part of
> the graph and have specific children that live under 'involved in
> morphogenesis terms'.
>
>
>
>
> Midori Harris wrote:
>
> Yup, I think we're converging on a revised model nicely here.
>
> We do still have to consider whether anatomical structure
> formation can still stay under developmental process, in light
> of our emerging agreement that cellular component assembly is
> sometimes -- but not always -- developmental, and we haven't
> questioned (second-guessed) our decision that a CC is_a
> anatomical structure. The implication is that anatomical
> structure formation is not always developmental, and we need new
> terms.
>
> m
>
> On Tue, 18 Nov 2008, David Hill wrote:
>
> Tanya talked to me about this issue yesterday. I share her
> concerns and I think that this is why we have a term for
> cellular structure morphogenesis [GO:0032989]
> <http://www.informatics.jax.org/searches/GO.cgi?id=GO:0032989#top>
> and a term for cellular component organization [GO:0016043]
> <http://www.informatics.jax.org/searches/GO.cgi?id=GO:0016043#top>
> in the first place. The morphogenesis term is a
> developmental process. I think the key distinguishing factor
> is that development is a progression of the cell over time,
> from an immature state to a mature state if you will. Some
> of the terms that Tanya points out don't reflect that. They
> are things that happen in a cell as just part of its routine
> being. I think actin cortical patch formation would
> certainly work for this. So the bottom line is, I take back
> what I suggested yesterday.
>
> I do think that in some cases the assembly of a cellular
> component is in fact a developmental process. It's when it
> also is part of the progression of the cell over time from a
> less mature to a more mature state. I know it's a fine line,
> but it's certainly a line. Hey, that's why we work as a team!
>
> David
>
> Midori Harris wrote:
>
> Well, it's pretty much consistent with what I alluded to
> much more briefly in my last contribution to this
> thread, so I'm also keen to hear what David and Tanya
> have to say about it.
>
> m
>
> On Tue, 18 Nov 2008, Jennifer Deegan (nee Clark) wrote:
>
> Hi Tanya,
>
> Are you saying that you don't feel that the process
> by which subcellular components are generated should
> really be is_a to developmental process? I feel
> this, but I'm not sure whether I have missed some
> intention you had in making this graph, as the
> developmental process def currently does include
> subcellular structures:
>
> def:A biological process whose specific outcome is
> the progression of an integrated living unit: an
> anatomical structure (which may be a subcellular
> structure, cell, tissue, or organ), or organism over
> time from an initial condition to a later condition.
>
> To my mind it would make more sense somehow to
> distinguish between the kind of multicellular
> structures that undergo classical developmental
> processes, and the subcellular structures that are
> generated in different ways. If my understanding is
> correct then I think maybe the answer is just to do
> something like this:
>
> [i]anatomical structure generation (renamed from
> anatomical structure dev)
> ---[i]multicellular structure development (classical
> organ and tissue and larger scale developmental
> processes)
> ---[i]cell development (to include things like cell
> differentiation as now)
> ---[i]subcellular structure generation
>
> [i]developmental process
> ---[i]multicellular structure development (classical
> developmental processes)
> ---[i]cell development (to include things like cell
> differentiation)
>
> This would take CC assembly out of under
> development, but keep it under anatomical structure
> generation. It would also avoid massive
> rearrangements of the development/morphogenesis
> structures that were so carefully put together
> before. Does that make sense or have I missed something?
>
> Thanks,
>
> Jen
>
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>
>
> --
> David P. Hill, Ph.D.
> Bioinformatics Scientist: Ontology Development
> Gene Ontology Consortium
> The Jackson Laboratory
> www.geneontology.org <http://www.geneontology.org>
> www.informatics.jax.org <http://www.informatics.jax.org>
>
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>
>
>
> --
> Tanya Berardini
> TAIR Curator
> www.arabidopsis.org <http://www.arabidopsis.org>
>
>
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Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium
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