developmental parent of cell structure mor

[gocentral]

cellular structure morphogenesis The process by which cellular structures are generated and organized. Morphogenesis pertains to the creation of form.

Has a development parent, which seems incorrect for this process.

this need not be related to developemt in a unicellualr organism (for example during vegetative growth)

Val

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/5117":https://sourceforge.net/p/geneontology/ontology-requests/5117

[gocentral]

Logged In: YES user_id=436423 Originator: NO

The relationships fit the definitions, though: anatomical structures can be subcellular, and morphogenesis is always a type of development (and development is "the progression of x over time, from an initial condition to a mature state").

Original comment by: mah11

[gocentral]

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David agrees that the defs and relationships are OK as they are -- development can take place at the scale of a subcellular anatomical structure. We can add a bit to the def of 'developmental process' to avoid ti being mistakenly thought to exclude subcellular structures.

Original comment by: mah11

[gocentral]

• labels: --> Other term-related request
• assigned_to: nobody --> gomidori
• milestone: --> 224410

Original comment by: mah11

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Logged In: YES user_id=516865 Originator: YES

I still think there is a probelm here for single cells.

I asked Jacky Hayles at Cell Cycle Laboratory Cancer Research UK, London Research Institute

who is an expert in morphogeneis in S. pombe. This is her response. I'd be interested what other single-celled organism curtors think.

Val

From Jacky "Single cells definitely undergo shape changes eg shmooing for conjugation and this is a form of development. Many morphogenesis genes (tea1, pom1 etc) are required to maintain the normal cell shape which I wouldn't classify as development"

Original comment by: ValWood

[gocentral]

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But it all still fits the definitions -- the thing that's developing doesn't have to be a whole cell; it can be any anatomical structure, and in GO 'anatomical structure' is defined as encompassing subcellular structures ("Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.").

m

Original comment by: mah11

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I don't know what the problem is but it does cause problems for us. I can only think that it is a difference between single celled orgs and multicellualr orgs.

For example Jack works on genes which are involved in normal cell polarity and morophogenesis (but are not involved in any aspect of development). They are just involved in maintaining normal cell shape during vegtative growth. We don't think of this as development but according to GO it is.

I'm stuggling with this part of the definition "progression of an integrated living unit: a cell, tissue, organ, or organism over time from an initial condition to a later condition" because during the maintenece of noraml cell shape there is no initial condition or later condition.

I know I've been here before, but the penny hasn't dropped yet. Maybe I'm missing something or i used the wrong terms or something?

Original comment by: ValWood

[gocentral]

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I'm finding something else odd about this.

Cell morphogenesis is defined as Any process that modulates the size or shape of a cell.

but in that case, why doesn't it have 'regulation of cell growth (for example) as a child? It seems that is should be from the defs.

(this might me something to do with me not understanding the difference between modulates and regulates.....)

Original comment by: ValWood

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I've just extended the definition of developmental process (will be committed tonight) so it now says an integrated living unit is "an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism".

For a whole cell, polarity and shape have to be established, even during vegetative growth. Creating that shape is a type of morphogenesis, and therefore fits into development as it's defined.

The problem really seems to be that 'maintenance of cell polarity' is an is_a child of 'establishment and/or maintenance of cell polarity' -- it probably ought to be part_of, because an instance of maintaining cell polarity is not an entire process of establishing and maintaining cell polarity (contrast 'establishment of localization' and 'maintenance of localization', which are part_of localization). I'll bring this up with David.

David and Tanya will fix the cell morphogenesis definition when they do SF 1990703.

Original comment by: mah11

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OK 2 things will fix this

we ned to make sure that all cellular terms which have developmental process in their ancestry have GO:0048869 cellular developmental process in their ancestry also. ~We added this to something, was it cell morphogenesis? is there anything else?

2. maintence terms need moving out from morphogenesis. pending

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=1510062 Originator: NO

Hi,

The SGD curators met to discuss this and we would prefer that the tree structure remain as it is. The feeling here is that morphogenesis encompasses being able to maintain a formed shape (e.g. prevention of going back to the way you were) and not just the active process of forming it. We're okay with it having the developmental parent as with changing the relationship of the 'maintenance of polarity' term to a part_of child instead of an is_a child of 'establishment and maintenance'.

-Julie

Original comment by: juliep

[gocentral]

We have a plan for these terms that will let us address Val's concerns; background and specifics are in the email archive:

http://fafner.stanford.edu/pipermail/ontology-editors/2009-February/000387.html

Once that work is done, it may fix this anyway; if not, it will make any further fix-it work possible.

We've also decided that maintenance and morphogenesis are siblings, and organization is the parent that encompasses both forming a structure of a given shape and maintaining it. See the wiki:

http://wiki.geneontology.org/index.php/Cellular\_component\_processes (bottom of page)

Original comment by: mah11

[gocentral]

David - is this the one you wanted to take? m

Original comment by: mah11

[gocentral]

• assigned_to: gomidori --> ukemi

Original comment by: mah11

[gocentral]

Tanya and I tried to fix this last week. Our decisions were primarily based on the comments by Julie. We made a new term called 'cellular component assembly involved in morphogenesis' that was meant to reflect 'The feeling here is that morphogenesis encompasses being able to maintain a formed shape'. We also moved anatomical structure formation out from under development. We then tried to separate all of the existing cellular component assembly terms to be either children of this term, or the regular non-developmental 'cellular component assembly' term.

So now, if the cellular component assembly is one of the transient structures that forms, such as a pseudopod, it should go under 'cellular component assembly' (note, we still have to work on the cell projection terms). If it is a more lasting structure, like an axon, then it will get the morphogenesis parent.

Please let us know if you think we put any of the terms in the wrong place by telling us the term, and the parent that it should be placed as a child of. You can just e-mail us and we will fix it.

David

Original comment by: ukemi

[gocentral]

• status: open --> closed-fixed

Original comment by: ukemi

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11