histogenesis

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From: [ 1262269 ] *genesis http://sourceforge.net/tracker/index.php? func=detail&aid=1262269&group_id=36855&atid=440764

1) histogenesis: The origin and formation of tissues, that is of homogenous set of cellular type.

Therefore organogenesis is not a morphogenesis. Could-be part-of it, if one changes the definition of morphogenesis to include cell differenciation.

And "neural plate formation" should not be part-of "neural plate morphogenesis". On the contrary "neural plate morphogenesis" should be part of "neural plate formation", that would also include neuroblast differentiation for instance.

neurogenesis and gliogenesis should be "is-a" children of histogenesis, and not of organogenesis

2) suppress the parentage of GO:0009888: histogenesis.

GO:0009888: histogenesis becomes part-of 'organ development'

In general, all the branches should be followed until the end, to check that all sub-classing actually describe a "morphogenesis", that is a change of form. If a term describes a cell differenciation, it should be moved to the lineage "histogenesis".

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/2872":https://sourceforge.net/p/geneontology/ontology-requests/2872

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J Clark

>>It's what's left of the *genesis item moved to a new place. I'm not absolutely >>clear about what you're asking me to do, and would appreciate some clarification.

Well, I still don't agree that "histogenesis" is part-of "organ morphogenesis" and therefore of "morphogenesis" by inheritance.

It should be directly part-of "organ development".

Again, histogenesis is the formation of a tissu, while morphogenesis is the generation of shape. Those terms are orthogonal. They can't be linked together.

Some histogenesis do not involve changes of shape, and some changes of shape do not involve the development of tissu.

Another example in addition to my usual blood one: the histogenesis of sperm is not part of the morphogenesis of testicle. However, the morphogenesis of sperm is part-of the histogenesis of sperm. sperm is a tissue. Testicle is an organ.

Original comment by: lenov

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I don't see why histogenesis cannot be linked with morphogenesis. Doesn't the generation of tissue require some sort of change in shape? Can you think of an example where there is generation of a tissue in which there are no morphogenetic movements?

Original comment by: kpilcher

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Also, not all cell type differentiation terms should go under 'histogenesis' since not all cell types are part_of tissues. For example:

sporulation ; GO:0030435 (synonyms: spore differentiation, spore formation)

In Dicty, spore differentiation occurs, but the spores are not part_of a tissue. I'm sure this is true for yeast, although yeast has a separate sensu term. I imagine there are many other cell type differentiation terms that should not go under histogenesis.

Original comment by: kpilcher

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I agree with this point. Specific cell type differentiation terms should go under specific types of histogenesis. Not all cell differentiation should go under histogenesis.

Original comment by: ukemi

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> I don't see why histogenesis cannot be linked with > morphogenesis.

Because they are orthogonal! Even if all tomatoes are red, red is not a tomatoes or part-if a tomatoes.

> Doesn't the generation of tissue require > some sort of change in shape? Can you think of an example > where there is generation of a tissue in which there are no > morphogenetic movements?

Generation of the lymphocytes, or of sperm. CAUTION: There IS a change of CELL shape, but not of the TISSUE shape. And histogenesis characterise a tissue.

> Specific cell type differentiation > terms should go under specific types of histogenesis. Not > all cell differentiation should go under histogenesis.

Yes of course. Never said the contrary. I was actually the one asking for the move of neurogenesis, gliogenesis etc. as is-a children of histogenesis.

Could-we focus on the point here. GO is about semantics. Morphogenesis is a change of shape. Histogenesis is the development of a tissue. No logical relationships. The fact that "histogenesis" and "organ morphogenesis" can be both part of "organ development" does not imply they a relationships together.

Original comment by: lenov

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I thought that histogenesis was just development of a tissue. If it is then it should be like this:

[i]development (of an entity) ---[i]histogenesis (development of a tissue) ------[p]tissue morphogenesis ---[i]cell development (development of a cell) ------[p]cell morphogenesis ---[p]morphogenesis ------[p]tissue morphogenesis ------[p]cell morphogenesis

Do I understand correctly that you say that a dispersed tissue like blood in hemopoeisis does not have tissue morphogenesis because it is dispersed? I would have thought that there must be some process that leads to its being dispersed and that is the morphogenetic step.

Thanks,

Jen

Original comment by: jenclark

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I am also not completely convinced by the blood argument. Although mature blood cells are freely dispersed, during the development of the tissue there must be some kind of morphogenesis. Could the actual release of the cells into the bloodstream be considered a morphogenesis? They are going from a stromal organization to being freely floating.

David

Original comment by: ukemi

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"I am also not completely convinced by the blood argument. Although mature blood cells are freely dispersed, during the development of the tissue there must be some kind of morphogenesis. "

Maybe. But this is irrelevant. Even if you're right, that does not make histogenesis "part-of" morphogenesis.

"Could the actual release of the cells into the bloodstream be considered a morphogenesis? They are going from a stromal organization to being freely floating."

Yep. And then, lymphoid (not blood. Blood is an organ, not a tissue) morphogenesis would be part-of lymphoid histogenesis. Not the contrary.

Jen, I entirely agree with your structure. Add "organ morphogenesis" as a type of "morphogenesis".

And then we'll have to put the links between "XXX developement", "XXX morphogenesis" and "YYY histogenesis", where XXX is an organ, and YYY is one of the tissues composing the organ.

Original comment by: lenov

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I think the thing that was throwing me off a bit was the term 'histogenesis' itself. Whenever I see 'genesis' in relation to a developmental process I automatically think of morphogenesis (for example, when I think of organogenesis I immediately associate it with morphogenetic events). Perhaps the term 'histogenesis' should be 'tissue development' (synonym 'histogenesis') to reduce confusion. Also, this would parallel the cell development/morphogenesis:

---[i]tissue development (development of a tissue) ------[p]tissue morphogenesis ---[i]cell development (development of a cell) ------[p]cell morphogenesis

Original comment by: kpilcher

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Maybe I am confused, but I thought our original plan was to move histogenesis to be a child of organ development (organogenesis) in the same way that we had originally moved organogenesis out from under morphogenesis. Then we were to create a tissue morphogenesis term. The plan was that we were going to do this systematically to clean up an original mixing of development and morphogenesis terms for all of the anatomical differentiae under development and morphogenesis. . If you look at the is_a children of histogenesis, you see that they are in fact development terms.

So I think we are in fact on the same page. The work just isn't completed yet.

David

Original comment by: ukemi

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Yes that's a possibility. Nicolas said something in point 2 above about following all branches and I wasn't clear on what he meant. That might have been it.

So I've just to make 'histogenesis' become 'tissue development' and then make a new 'tissue morphogenesis' term and fit them all together then? That would be easy.

Jen

Original comment by: jenclark

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I think Karen and I were typing at the same time.

"I think the thing that was throwing me off a bit was the term 'histogenesis' itself. Whenever I see 'genesis' in relation to a developmental process I automatically think of morphogenesis (for example, when I think of organogenesis I immediately associate it with morphogenetic events)."

You are not alone. This difference in thought was and still is reflected in the ontology. That is why we need to clean it up. Remember at the Caltech Go meeting we had a big discussion about this. The clearest proposal perhaps:

1) For all terms other than morphogenesis, create a term called XXX development and make the genesis term a synonym. 2) Create a morphogenesis term for all *s that take on a shape.

To sort this out, use the current definitions to determine where existing terms fit.

David

Original comment by: ukemi

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Hi,

Yes that seems good. I hadn't realised that Nicolas was talking about things that we already knew. He's visited my office to say we're all on the same page now and that he'll leave us to sort it out.

Jen

Original comment by: jenclark

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Great. Tell him to keep an open eye and let us know if he spots something amiss.

Karen, from your last e-mail I assume you ar ok with this too.

David

Original comment by: ukemi

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Yes, it sounds good to me.

Hope you don't mind my chiming in even though I'm not officially part of the development group!

Karen

Original comment by: kpilcher

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Hi Karen,

No we don't mind at all, it's great to have you involved. :-)

Thanks,

Jen

Original comment by: jenclark

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with reference to comment of 2005-09-28 15:53: Shall I make the structure like this:

1)

[i]development (of an entity) ---[i]organ development ---[i]histogenesis (development of a tissue) ---[i]cell differentiation

or

2)

[i]development (of an entity) ---[i]organ development ------[i]histogenesis (development of a tissue) ---[i]cell differentiation

I'm wondering whether there is an example of tissue developing without being part of an organ just as there are examples of cells differentiating without being part of an organ or tissue?

Also the current def of histogenesis is 'The origin and formation of tissues.' If I've to make it so that 'histogenesis' is a development term then that means that I have to obsolete and make a new one, since this is currently defined as a formation term. Would you agree? If this is the case then I need to send an obsoletion warning and give two weeks delay.

The discussion of this from the meeting is at http://www.geneontology.org/minutes/20050408\_Pasadena.txt (search on 'morphogensis')

Thanks for the feedback.

Jen

Original comment by: jenclark

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Hi Jen,

I cannot think of a tissue that develops independently of an organ, so I would opt for #2. However, we should wait for the dicty people. They may consider the structures in the fruiting stage tissues, but not organs. We also may want to make tissue development the primary term and histogenesis the synonym to make is consistent with organogensis.

We should also carry on with the initial plan from Pasadena to sort out all of the development/morphogenesis terms right down the graph.

David

Original comment by: ukemi

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Hi David,

Thanks, yes that all sounds good. I am still plodding through fixing the development/morphogenesis terms. It gets a bit pushed to one side by millions of other things but I'm still on it. Histogenesis will be quite straightforward since the child terms are okay.

Thanks,

Jen

Original comment by: jenclark

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Option 2 is good.

Dicty does not have tissue, only differentiated cell types, and so this is not a problem for us.

Karen

Original comment by: kpilcher

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Jen,

I don't know what I was thinking this morning. Endoderm, ectoderm and mesoderm are primary germ layer tissues that are not part of an organ! So the option where there terms are sibs are better! Sorry!

David

Original comment by: ukemi

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Well spotted there. Thanks for getting back to me with that. :-)

Jen

Original comment by: jenclark

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I don't need to obsolete this one do I? The annotations will still be correct since the term is being redefined as a term that would be an ancestor of the term with the old def. It's ages since I moved a term up like this so I'd forgotten.

Jen

Original comment by: jenclark

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Hi Jen,

You should check the minutes from the CalTech meeting. I remember we talked about whether these types of things needed to be obsoleted. In this case, I think it was one of those deals where it was simply a mistake in the ontology to put it where it is, so it just needs to be moved and renamed. Check with Midori to see if she thinks it warrants an obsoletion. From an animal perspective since we have lots of "development" terms under histogenesis, this seems clear. Check the plant terms and be sure this is o.k. Also please remember to make a tissue morphogenesis term. I think morphogenesis of an epithelium should be an is_a child of this.

David

Original comment by: ukemi

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Hi David,

I think that the histogenesis term is currently clearly defined and positioned as a formation term. Changing this to make it a development term is clearly a significant change but the meeting minutes say that I only need to obsolete if there is any risk that the annotations would become wrong as a consequence of the change. I'm moving the term up the graph so if annotators have used the term as a formation term then the annotations will still be correct and will just be a bit less specific. This means I shouldn't have to obsolete. This is the rule that Midori explained to me when I first started fixing the development node and it hasn't changed but I just had to get it fresh in my mind again since I haven't done this kind of move for a while. That's why I was writing to check.

I think it will be fine just to redefine, both by usual practise and by the rule that was established at Caltech.

Midori, would you agree?

Thanks,

Jen

The Caltech minutes are at http://www.geneontology.org/minutes/20050408\_Pasadena.txt and the section is found by searching on 'morphogenesis'.

Original comment by: jenclark

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Midori says it's cool just to fix the term without obsoleting.

Jen

Original comment by: jenclark

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Okay that's done now.

Jen

Original comment by: jenclark

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• status: open --> closed-accepted

Original comment by: jenclark

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• assigned_to: Jennifer Deegan --> nobody
• Group: Plant Ontology --> None

Original comment by: cooperl09