lymph gland/node development

[gocentral]

Hi,

Can these both be children under a new term 'gland development'?

lymph gland development (sensu Arthropoda) ; GO:0048542 lymph node development ; GO:0048535 synonym: lymph gland development

Thanks,

Jen

(I'll write to Alex to ask him to look at this.)

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/2921":https://sourceforge.net/p/geneontology/ontology-requests/2921

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Jen,

According to Stedman's Medical Dictionary, a gland is defined as "An organized aggregation of cells functioning as a secretory or excretory organ."

I don't know how you were intending to define gland for the GO, but lymph nodes are not "glands" according to this definition, and I believe that the lymph glands of insects are not "glands" either, but rather the site of hematopoiesis in those organisms. I suspect the labeling of these organs as glands reflects some aspect of gross morphology in the early days before their actual functions were appreciated.

I don't know why there necessarily should be a gland development term per se in the GO, apart from lexical grouping, as it strikes me that the processes that are involved in the formation of true glands may themselves be quite diverse, as their morphology does vary.

Thus, I would vote against a "gland development" term in the GO. We already have a much better term, GO:0035270 endocrine system development, as parent to some of the gland terms.

-- Alex

Original comment by: addiehl

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Hi Alex,

Thanks for your feedback. I'll remove those child terms. I've written to David to get his opinion on the gand development term too. If he agrees that there's no need for it then I can remove it.

Thanks,

Jen

Original comment by: jenclark

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Hi Alex,

I was thinking about your argument against 'gland development'. Wouldn't the same argument stand against 'organ development' since they come in all shapes and sizes, but we still have that term.

I'm not sure whether that means that organ development is good or that gland development is bad but I'm working on it. :-)

Jen

Original comment by: jenclark

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Hi Jen,

I just checked our anatomical dictionary and there is not a grouping term called gland. As Alex points out, most of the glands are either under endocrine system or the anatomical structure for which they are a part. I think GO should remain consistent with the anatomies.

David

Original comment by: ukemi

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Hi Jen,

Just to reiterate the point, if one defined gland development as "development of a secretory or excretory organ" in order to make a GO term (matching the dictionary definition), neither lymph node development or lymph gland development (sensu Arthropoda) would be proper children, since they are not secretory or excretory organs. This would only lead to confusion for GO users and OBOL.

I think this is an example of a clash between the precise usage of a term, and its misapplication in the past due to ignorance, or its commonplace versus scientific usage (consider the word 'theory' in the context of the teaching of evolution in the US). Lexical grouping terms have their uses, such as organ development, when the definition is sufficiently broad to match both an accepted definition of the term and its past usage (and of course we had to broaden the definition of organ in the GO), but when an acceptable definition of the term does not match its past usage, it is perhaps best to avoid the term in the GO.

-- Alex

Original comment by: addiehl

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So:

1) Alex is saying that we can have 'gland development' as long as it just includes only secretory or excretory organs and does not include lymph glands and nodes (this preferred setup is what I have in there just now).

2) David is saying that we shouldn't have a gland grouping term since the anatomy dictionary doesn't have one.

Is that right?

I'm not sure about leaving out the gland grouping term just because others don't have it. I think it's just as valid as organ development and allows users to find all the developmental processes for the different types of secretory and excretory organs all together, which might be handy. Is there any other reason why it shouldn't be there?

Thanks,

Jen

Original comment by: jenclark

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Jen,

I would prefer not to have the term at all, but if you insist, why not make the term "secretory or excretory organ development" and use "gland development" as some kind of synonym. That way you avoid the lexical issues with the term name, and make it clear just what kind of functions are involved. Also, having the synonym would allow searches to come up with the term.

-- Alex

Original comment by: addiehl

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That's a thought.

I'm not sure about the excretory bit. That makes me think of something else that definately isn't a gland. Secretory might be good though. The thing is, aren't there bits of the body that secrete even though they aren't glands? For example the stomach lining by a certain view of it might secrete acid. But that's hydrogen ion pumping really isn't it? Are we entering tricky territory here because of the fine line between tissues that secrete substances and actual dyed in the wool type glands that squirt out hormones and things like that.

The glands we have are:

adrenal gland development mammary gland development prostate gland development ring gland development salivary gland development sebaceous gland development thyroid gland development

and a few more that are children of those.

Jen

Original comment by: jenclark

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I took the name from the definition I reported earlier. We can drop the "excretory" portion of the term name if you like.

As you point out, many cell types, tissues, and organs secrete things upon stimulation. I think you have to decide what really makes a secretory organ unique, and include it as part of the definition. Also, are there organs whose primary function is secretory, but are not actually called glands by their common name? They need to be children too.

-- Alex

Original comment by: addiehl

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Yes that's a good idea. I'll try to figure out what makes glands glands. Plants don't have many so I'm not super-familiar with them, but I do know of one tree in tenerife that has glands in the tips of it's leaves. They just stand around casually driping. I'm not sure why.

I'll look in books.

Jen

Original comment by: jenclark

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I've got a definition here that's a bit better.

deep breath...

A gland consists of one or more cells that make and secrete (export) a particular product. This product, called a secretion, is an aqueous (water- based) fluid that usually contains proteins, but there is variation - for example, some glands release a lipid- or steroid rich secretion. Secretion is an active process; glandular cells obtain needed substances from the blood and transform them chemically into a product that is then discharged from the cell.

Glands are classified based on site of release and relative number of cells forming the gland.

This book has diagrams showing the different structures of glands and they are either 'simple duct structure' or 'compound duct structure' with various subclasses.

Each developmental type has examples so e.g. simple tubular includes the intestinal glands, and compound alveolar includes the mammary glands.

I'd say that since there are particular morphological classes of glands then we probably ought to be able to have them in the ontology.

If you want to see the book it's called 'Human anatomy and physiology' fifth edition by Elaine Marieb.

Does that seem better?

Jen

Original comment by: jenclark

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Jen,

I think a key concept that needs to be included in the definition is that the primary function of secretory organs/glands is the secretion of some substance.

Also, there are gastic glands that secrete acid in the stomach; see PMID: 10960360, for instance (perhaps it's in the book you cite too).

-- Alex

Original comment by: addiehl

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Do you mean that I've missed the 'primary function' bit? The secretion bit seems quite clear from that def.

Jen

Original comment by: jenclark

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Yes, but we've already discussed that many cell types secrete various substances upon stimulation. T cells, for instance, secrete IL-2 and various other cytokines upon activation. By the definition given, they consititute a gland. It's not their only function, although certainly it's among their primary functions.

Mast cells secrete volumes of histamines and other soluble mediators upon activation, which is arguably their primary function. Are they a gland?

Neurons secrete various neurontransmitters upon activation. Are they a gland?

I think that the book definition of what a gland is, is very open to interpretation and does need further clarification.

Also, clear the definition allows the idea that a single cell can be a gland.
Can a single cell therefore be an organ?

-- Alex

Original comment by: addiehl

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Yes I see your point. Tricky.

The book says that there are lots of multicellular glands that are classified by their morphology and only one single celled gland. The single celled gland is a unicellular exocrine gland called a goblet cell. It's in the epithelial linings of the intestine and it secretes mucin.

It also says that glands can partly be defined by their mechanism of secretion. There are three sorts:

1) merocrine glands which secrete by exocytosis. 2) holocrine glands which secrete by cell rupture. 3) apocrine glands which secrete by pinching off the tip of the cell and allowing a small amoutn of cytoplasm to leak out.

Does that help?

Jen

Original comment by: jenclark

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Jen,

I know a gland when I see one, but I'm still not clear how to define it for the GO, nor is it clear to me that a secretory organ development/gland development term is a useful or needed parent for processes as diverse as the differentiation of goblet cells, thyroid glands, sebacious glands, and gastic glands and even the pancreas and liver, both of which possess glandular functions, and all of which are quite diverse morphologically, and may well originate from different embryonic tissue types through completely different processes.

Sorry to be such a stick in the mud, but I'm still looking for a unifying principle here.

-- Alex

Original comment by: addiehl

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Hi Alex,

Yes I see what you mean. Don't worry about the apparent disagreement. I'm really enjoying having the chance to discuss this properly. I wish I could pin the gland def down perfectly but if I can't then that's cool and I'll obsolete.

It seems to me that exactly the same problems that you mention also affect organ development and that worries me a bit. Does that mean that we shouldn't have either term?

Thanks,

Jen

Original comment by: jenclark

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I don't really want to go near 'organ development' apart from saying that its definition is sufficiently broad to cover all its children without potentially covering additional children that for reasons not stated, we choose not to define as organs (ie. would we make liver development or pancreas developmen children of gland development, or mast cell differentiation).
'Organ development' is a nice grouping term at least partly for the preceeding reason.

-- Alex

Original comment by: addiehl

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So really the problem is just that we need a definition for gland development that excludes pancreas development and mast cell differentiation and things like that?

Jen

Original comment by: jenclark

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Yes, but in an elegant way.

-- Alex

Original comment by: addiehl

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Okay, I'll shoot for inelegant and we can go from there. :-)

Jen

Original comment by: jenclark

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My book says 'the pancreas is a mixed gland composed of both endocrine and exocrine gland cells.' So maybe the definition shouldn't exclude the pancreas. What do you think?

Jen

Original comment by: jenclark

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I would favor inclusion of the pancreas. The liver is a bit trickier.

-- Alex

Original comment by: addiehl

[gocentral]

• priority: 5 --> 1

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

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• priority: 1 --> 5
• status: open --> closed-fixed

Original comment by: jenclark

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

Original comment by: cooperl09