tissue polarity query

[gocentral]

In the GO tree at the moment, we have 'establishment and/or maintenance of cell polarity' and 'establishment and/or maintenance of cytoskeleton polarity'.

But we only have 'establishment of tissue polarity'.

Chihiro in FlyBase is curating a Dev. Biol. paper about a gene product involved in maintaining the distal orientation of wing hairs (an example of tissue polarity).

(see PMID: 15501220)

There doesn't exist an appropriate GO term for this at the moment- therefore I'd like to make a new term 'maintenance of wing hair orientation'. But currently there's no nice parent to put this under.

Is it ok to create the terms:

establishment and/or maintenance of tissue polarity ; GO:NEW --%establishment of tissue polarity ; GO:0007164 ----%establishment of planar polarity ; GO:0001736 ------%establishment of wing hair orientation ; GO:0001737 --%maintenance of wing hair orientation ; GO:NEW

Is this allowed with the phasing out of and/or terms? i can create the inbetween terms if neccessary too- eg establ. and/or maint. of planar polarity etc.

Also: what's the difference between tissue polarity and planar polarity? I was reading around to try and come up with a definition for GO:0007164, but kept ending up with the same wording as the definition of planar polarity in GO:0001736.

thanks, Becky

Reported by: beckyfoulger

Original Ticket: "geneontology/ontology-requests/2200":https://sourceforge.net/p/geneontology/ontology-requests/2200

[gocentral]

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Hi Becky,

I'm not keen on establishment and/or maintenance terms. How about having "development of tissue polarity" instead. I think it fits with the standard def for development. Then that term can include establishment and maintenance.

I also think there are probably examples of tissue polarity that are not planar. Although out of my league, I think in the meristem of plants, there is polarity, but it is not necessarily planar.

Original comment by: ukemi

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Hi David,

Thanks for your suggestion- do you mean:

wing morphogenesis ; GO:0007476 --%maintenance of wing hair orientation ; GO:NEW --%establishment of wing hair orientation ; GO:0001737

cytoskeleton organization and biogenesis ; GO:0007010 --%development of tissue polarity ; synonym: tissue polarization ; GO:NEW ----%establishment of tissue polarity ; GO:0007164 ------%establishment of planar polarity ; GO:0001736 --------%establishment of wing hair orientation ; GO:0001737 ----%maintenance of wing hair orientation ; GO:NEW

term: development of tissue polarity ; GO:NEW exact synonym: tissue polarization def: Processes aimed at the polarization of cells over time. This includes both the establishment of tissue polarity and maintaining the polarity once it has been set up.

thanks, Becky

Original comment by: beckyfoulger

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I like David's idea of switching this to development too but I'm not sure how easy it is to make the current standard definitions fit with the idea of development of polarity. The current development defs discuss development of a structure and don't leave a lot of room to work in the idea of just the polarity of a structure.

For example, for multicellular structures we could have something like this:

%development of tissue polarity synonym: establishment and/or maintenance of tissue polarity

Def: Processes aimed at the progression of a tissue over time, from its formation as an apolar structure to the mature polar structure. Polarity refers to the tendency of an organism to develop differentially along an axis.

For subcellular structures we could have this:

%development of neuroblast cell polarity synonym: establishment and/or maintenance of neuroblast cell polarity

def: Processes aimed at the progression of a neuroblast cell over time, from initial commitment of the cell to a specific fate, to the fully polar cell.

I'm not sure that these definitions really make it clear that we're talking about just the development of polarity in these structures. Is there a good way round that d'y think?

If Becky wanted to implement her suggested term while we talk this over I'd be happy for her to do that so we don't hold up the annotation.

For the planar polarity question, there are definately examples of polarity that are not planar. It sounds as if the planar polarity is refering to the polarity in a thin layer of cells, but there is establishment of polarity in the drosophila embryo by bicoid and the embryo is not planar. Would that be a reasonable counter example?

for a def of establishment of tissue polarity term how about: Coordinated organization of groups of cells in a tissue, such that they all orient, and can develop differentially, along an axis.

Jen

Original comment by: jenclark

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Hi Jen,

I think these defs encompass too much of the whole of development.

How about: Def: Processes aimed at the progression of tissue polarity over time, from an original apolar structure to the mature polar structure. Polarity refers to the tendency of an organism to develop differentially along an axis.

def: Processes aimed at the progression of neuroblast cell polarity over time, from an initial non-polar cell, to the fully polar cell.

Don't these fit with the development of a structure concept? They just describe a certain aspect of the development of the structure.

David

Original comment by: ukemi

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Yes that sounds good. :-) Would it be a bit like this then?

[i]development of embryo polarity ---[p]establishment of dorsal embryo domain ---[p]maintenance of dorsal embryo domain

Jen

Original comment by: jenclark

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Yes, except for the graph below, I would add even more parents:

[i]development of embryo polarity ---[i]development of dorsal/ventral embryo polarity ----[p]establishment of dorsal/ventral embryo polarity ------[i]establishment of dorsal embryo domain ----[p]maintenance of dorsal/ventral embryo polarity ------[i]maintenance of dorsal embryo domain

And, I suppose we would want to have these be is-a children of the generic axis specification terms. That part of the graph may need to be expanded.

Original comment by: ukemi

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Yes I like the look of that. :-)

Becky since you're disappearing soon do you want me to assign this to myself or were you going to do it before you go?

Jen

Original comment by: jenclark

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If you're happy to take this on Jen- that'd be great. thanks. Is it ok if i add in a 'maintenance of wing hair orientation' new term for Chihiro under the recently added 'wing hair organization and biogenesis' term for the moment. This shouldn't affect the new structure you and David suggest. Becky

Original comment by: beckyfoulger

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Thanks, I'll take it over then. I think that would be a good idea for you to add that term in since we're not meant to do big switch-arounds too quickly. I can fix it up once all the discussion's done.

Jen

Original comment by: jenclark

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• assigned_to: nobody --> jenclark

Original comment by: jenclark

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I've added in the new term needed for Chihiros curation: wing hair organization and biogenesis ; GO:0035317 --<maintenance of wing hair orientation ; GO:0035321 (NEW)

When the polarity section is worked out, it will need to be added to the polarity node of process too. thanks, Becky

Original comment by: beckyfoulger

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When I do this I also need to look at how the descendants of establishment of tissue polarity ; GO:0007164 relate to id: GO:0048560 establishment of anatomical structure orientation. I'm moving this to here so I can close [ 1002567 ] orientation https://sourceforge.net/tracker/index.php? func=detail&aid=1002567&group_id=36855&atid=440764 which is otherwise complete.

Jen

Original comment by: jenclark

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Hi,

This item has been open for a long time. Please comment to let us know whether you would like it to remain assigned to you, or would prefer it to be reassigned. (You don't necessarily have to work on it immediately if you keep it; we just need to know whether it's still on your list.)

Thanks, Midori & David Ontology development group managers

Original comment by: mah11

[gocentral]

• status: open --> closed-out-of-date

Original comment by: jenclark