maintenance of 'x' identity

[gocentral]

Hi,

I was just looking at the maintenance of meristem identity terms and related terms made for plant meristems. I'm writing the documentation for the development node just now:

http://www.ebi.ac.uk/~jclark/GOwebsite/development\_folder/ GO.process.guidelines.html

and I'd like to work out how these terms fit in with the standard development terms.

I guess the term:

meristem organization ; GO:0009933

is analagous to the standard term:

"x" structural organization Biological processes that contribute to the act of creating the structural organization of "x". This process pertains to the physical shaping of a rudimentary structure.

If this is correct then I could add this as an exact synonym so Chris's term decomposition knows what it's dealing with.

I'm not sure that we yet have a standard term for maintenance of cell or tissue identity, like this one:

maintenance of floral meristem identity ; GO:0010076

Shall I make one?

Thanks,

Jen

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/1776":https://sourceforge.net/p/geneontology/ontology-requests/1776

[gocentral]

Logged In: YES user_id=631592

I'm just beginning to think about this, but somehow I think at the cellular level, maintenance of identity would be related to cell fate commitment. I know in plants the whole idea of being committed to a certain fate is really different than it is in animals, because cell fates don't become so restricted. But right now, I think this type of term has to be related somehow to cell fate commitment. I think the structural stuff is fine.

Original comment by: ukemi

[gocentral]

Logged In: YES user_id=735846

Yes I'd agree that it could be thought of at the cell level. Plant scientists talk about 'meristem identity' which is a bit like talking about a tissue I suppose. The individual cells in the meristem must also all have meritem identity so it might be something like

%floral meristem development --<floral meristem morphogenesis ----<floral meristem formation ------<floral meristem cell differentiation --------<floral meristem cell fate commitment ----------<floral meristem cell fate specification ----------<maintenance of floral meristem cell identity ----------<floral meristem cell fate determination --------<floral meristem cell development

where: 'maintenance of floral meristem cell identity' refers to processes that ensure that the identity of the cell remains the same following specification. I'm not sure if maintenance of cell identity in plants is as permanent as cell fate determination. I'll go and read stuff.

Thanks,

Jen

Original comment by: jenclark

[gocentral]

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An alternative view in an e-mail from Becky:

Hi Jen,

A lot of the plant tissue specificity terms are under the existing 'specification of organ identity ; GO:0010092' term. So I'd agree with your suggestion to make a 'maintenance of organ identity ; GO:new' term undergo organogenesis too.

I think it should be kept separate from the maintenance of X cell identity terms though (eg maintenance of oocyte identity (sensu Insecta) ; GO:0016350).

thanks, Becky

Original comment by: jenclark

[gocentral]

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I'm OK with the meristem structural organization. Also the maintenance of x identity at the tissue level is OK. I would NOT add any of the cellular level terms, unless you can think of a specific example of a gene that would be annotated to it. I cannot think of one.

Original comment by: syrhee

[gocentral]

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I have added the synonym 'meristem structural organization' to 'meristem organization', and put in the generic term 'structural organization' as a parent, as stipulated in the development documentation. All the terms 'x structural organization' have been given the generic term as a parent as well.

New term:

[Term] id: GO:0048532 name: structural organization namespace: biological_process def: "Processes that contribute to creating the structural organization of an organ or tissue. These processes pertain to the physical shaping of a rudimentary structure." [GO:curators] relationship: part_of GO:0009653 ! morphogenesis

This item is now finished so I'll close it.

Thanks,

Jen

Original comment by: jenclark

[gocentral]

• status: open --> closed-accepted

Original comment by: jenclark