neurogenesis

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We have:

GO:0007399 neurogenesis The origin and formation of nervous tissue.

The correct definition is: The process by which nerve cell are generated. This include the production of neuroblasts and their differenciation into neurons.

As such, neurogenesis should be child of histogenesis, not organogenesis (more later on that topic)

And it shouldn't have the following children:

central nervous system development (should be chid of a term "nervous system development" itself child of organogenesis)

establishment of blood-nerve barrier

gliogenesis (should be child of histogenesis)

neural tube formation (should be child of central nervous system development)

peripheral nervous system development (should be chid of a term "nervous system development")

stomatogastric nervous system development (should be chid of a term "nervous system development")

Reported by: lenov

Original Ticket: "geneontology/ontology-requests/2802":https://sourceforge.net/p/geneontology/ontology-requests/2802

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These sure seem like reasonable relationships to me! -Doug

Original comment by: doughowe

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This definition of neurogenesis is close (if not exact) to what we originally had, but based on the position in the graph and the way it is used in a lot of manuscripts, we changed it to the current one. If you look up neurogenesis in Gilbert, it says, "see neural development".

Perhaps we should change the current term name to neural development or nervous system development and keep the def the same. Then, we could create a new cellular term called neurogenesis with the appropriate parents and children.

Do you think gliogenesis should remain a part_of child of nervous system development and also be made an is_a child of histogenesis.

The rest of these relationships all look good! Thanks!

David

Original comment by: ukemi

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Hello,

In looking around for definitions of neurogenesis I find examples of both the original, broad definition and your more narrow definition; the broader definition slightly more often.

Perhaps the best comes from Henderson's Dictionary of Biological Terms (11th ed.). It has both: 'formation of the nervous system during development; development of nerves'

It seems to me that both definitions are 'correct'. The problem with changing GO:0007399 to the more narrow definition is that some model organisms (e.g. Drosophila) use 'neurogenesis' in the broader sense in their research and literature, and the current annotations reflect this.

If a term for the narrow definition of 'nerve cell generation' is needed then why not make the new term and make it a part_of child of GO:0007399, and leave the definition and parentage of GO:0007399 unchanged?

Russ

Original comment by: rtc26

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Russ,

The graph, the literature and our annotations all reflect the broader definition of the term as well. I really have no opinion of which way the terms and synonyms go in the end as long as the defs and the graphs are correct.

I am also having second thoughts about neural tube formation being a part of central nervous system development. In the back of my mind I knew there was a reason for this in the first place. The neural tube gives rise not only to the central nervous system, but also to neural crest cells, which are not part of the central nervous system. We may want to think about keeping neural tube formation out on its own and having its relationship to the central nervous system reflected in an anatomy ontology. If we want to put it under central nervous system development, then we have to remember not to relate neural crest formation to it in the future, otherwise we will create TPVs.

David

Original comment by: ukemi

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Re Davids comment: "Do you think gliogenesis should remain a part_of child of nervous system development and also be made an is_a child of histogenesis."

Yes, this seems reasonable to me. Surely gliogenesis is a part of nervous system development, and is also a specific instance of histogenesis.

-Doug

Original comment by: doughowe

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"If you look up neurogenesis in Gilbert, it says, "see neural development".

That's because Gilbert is not a neurobiologist and as most scientists confuses the adjectives "neural" and "neuronal"

For the most recent definition of neurogenesis, see Guo-li Ming and Hongjun Song (2005) ADULT NEUROGENESIS IN THE MAMMALIAN CENTRAL NERVOUS SYSTEM. Annual Review of Neuroscience Vol. 28: 223-250

"some model organisms (e.g. Drosophila) use 'neurogenesis' in the broader sense in their research and literature"

Not at all, see: Nicolas Bertrand, Diogo S. Castro & Franois Guillemot (2002). PRONEURAL GENES AND THE SPECIFICATION OF NEURAL CELL TYPES. Nature Reviews Neuroscience 3, 517-530

"Parallel studies in Drosophila and vertebrates have revealed that proneural genes are key regulators of neurogenesis, coordinating the acquisition of a generic neuronal fate and of specific subtype identities that are appropriate for the location and time of neuronal generation. "

See also Andreas Wodarz and Wieland B. Huttner (2003) Asymmetric cell division during neurogenesis in Drosophila and vertebrates. Mechanisms of Development. Volume 120, Issue 11

"Perhaps the best comes from Henderson's Dictionary of Biological Terms (11th ed.). It has both: 'formation of the nervous system during development; development of nerves""

This is a layman definition. For a neurobiologist, the 'nerves' do not even contain neuronal bodies, only processes and support cells. The development of 'nerves', and the generation of neuronal bodies are two completely different biological processus, taking place at different times, and regulated by different mechanism (we should launch soem deep reflection on that at some point).

Original comment by: lenov

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I agree about the neural tube formation. It should be part-of
"nervous system development", not "central nervous system development" as I suggested.

Original comment by: lenov

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Nicholas,

I agree that there are two common usages of the term neurogenesis, one used by developmental biologists and one used by neurobiologists. I still think that a good solution would be to change the current neurogenesis term to nervous system development with neurogenesis as a synonym. Then, to create a new term neurogenesis that reflects the neurobiologists' definition that you point out. Would everyone be happy with this?

David

Original comment by: ukemi

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This solution is indeed the right one. So the children of GO:0007399 remain mostly correct.

Original comment by: lenov

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David,

This more or less what I suggested in my first post. So yes, this 'layman' is happy with you proposal.

Russ

Original comment by: rtc26

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Original comment by: jenclark

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Re Nicolas' statement: "This is a layman definition. For a neurobiologist, the 'nerves' do not even contain neuronal bodies, only processes and support cells. The development of 'nerves', and the generation of neuronal bodies are two completely different biological processus, taking place at different times, and regulated by different mechanism (we should launch soem deep reflection on that at some point)."

I agree completely. The terms 'nerve', 'neuronal', 'neural', and 'neuron' are not interchangeable, and should be used carefully because they are not always used properly in the literature.

I also agree that it would be prudent to change GO:0007399 'neurogenesis' to 'nervous system development' and then to create a new child term for true 'neurogenesis'.

Would the 'regulation of neurogenesis' terms stay where they are (and perhaps be renamed to 'regulation of nervous system development', etc..) or would they move to be children of the new 'neurogenesis'?? Based on their definitions, I think they would become children of the new 'neurogenesis'.

-Doug

Original comment by: doughowe

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I think we are all on the same page. I agree that nerve, neuron and neural all mean different and quite specific things. Just to be sure,

Nerve refers to the anatomical structure that contains the processes and the support cells, like the sciatic nerve and the optic nerve.

Neural refers to the nervous syatem.

Neuron refers to the cell type.

For the regualtion terms, I thik we need to look and see how they have been used for annotation. Clearly they have always been children, but the defs were not changed when we changed the definition of neurogenesis to reflect how we were actually using it. I suspect that they have probably been used to refer to neurogenesis as it is currently defined in the GO. One argument for changing the defs and creating new terms is the inclusion of glial types of things as children of the regulation terms.

For mouse, we have actually annotated to the children in all but one case. So, it wouldn't matter what the decision is, as long as the children got reassigned correctly.

David

Original comment by: ukemi

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Hi,

I've just been looking through this and summarising for myself the steps I need to take in implementation. The discussion is a little unclear so I have posted my summary below so you can all check that I've understood correctly what you mean. There are three sections marked 1-3. Any comments would be much appreciated.

For new folks

[i] means is_a [p] means part_of

Thanks,

Jen

1) First proposal:

neurogenesis ; GO:0007399 def: The origin and formation of nervous tissue.

suggested alternative definition:

The process by which nerve cell are generated. This include the production of neuroblasts and their differenciation into neurons.

Suggested change to parentage:

[i]histogenesis ---[i]neurogenesis

to:

[i]organogenesis ---[i]neurogenesis

Counter proposal

Change term name:

neurogenesis ; GO:0007399

to:

nervous system development ; GO:0007399 def: The origin and formation of nervous tissue. broad_synonym: neurogenesis

Add new term:

[i]nervous system development ; GO:0007399 ---[p]neurogenesis ; GO:new

neurogenesis ; GO:new def: The process by which nerve cell are generated. This include the production of neuroblasts and their differenciation into neurons.

'with appropriate parents and children'.

This counter proposal was accepted and can be implemented.

2) The changes in this section were suggested but I think have been shelved with the agreement of the above change to the neurogenesis term.

Suggest removing following child relationships:

[i]neurogenesis ---[i]central nervous system development ---[i]establishment of blood-nerve barrier ---[i]gliogenesis ---[i]neural tube formation ---[i]peripheral nervous system development ---[i]stomatogastric nervous system development

Suggest adding relationships:

[i]nervous system development ---[i]central nervous system development

[i]nervous system development ---[p]neural tube formation

*David not sure about this one.

[i]nervous system development ---[i]peripheral nervous system development

[i]nervous system development ---[i]stomatogastric nervous system development

[i]nervous system development ---[p]gliogenesis

[i]histogenesis ---[p]gliogenesis

3) I am still waiting for information on what to do about the child terms relating to 'regulation of neurogenesis'.

Original comment by: jenclark

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<YES> Counter proposal

Change term name:

neurogenesis ; GO:0007399

to:

nervous system development ; GO:0007399 def: The origin and formation of nervous tissue. broad_synonym: neurogenesis </YES> <YES> Add new term:

[i]nervous system development ; GO:0007399 ---[p]neurogenesis ; GO:new

neurogenesis ; GO:new def: The process by which nerve cell are generated. This include the production of neuroblasts and their differenciation into neurons. </YES> And this new "neurogenesis" term should be a "histogenesis".

<NO> [i]histogenesis ---[p]gliogenesis </NO>

gliogenesis is histogenesis, like neurogenesis. It is not part-of histogenesis.

Original comment by: lenov

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<YES> Counter proposal

Change term name:

neurogenesis ; GO:0007399

to:

nervous system development ; GO:0007399 def: The origin and formation of nervous tissue. broad_synonym: neurogenesis </YES> <YES> Add new term:

[i]nervous system development ; GO:0007399 ---[p]neurogenesis ; GO:new

neurogenesis ; GO:new def: The process by which nerve cell are generated. This include the production of neuroblasts and their differenciation into neurons. </YES> And this new "neurogenesis" term should be a "histogenesis".

<NO> [i]histogenesis ---[p]gliogenesis </NO>

gliogenesis is histogenesis, like neurogenesis. It is not part-of histogenesis.

Original comment by: lenov

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<YES> Counter proposal

Change term name:

neurogenesis ; GO:0007399

to:

nervous system development ; GO:0007399 def: The origin and formation of nervous tissue. broad_synonym: neurogenesis </YES> <YES> Add new term:

[i]nervous system development ; GO:0007399 ---[p]neurogenesis ; GO:new

neurogenesis ; GO:new def: The process by which nerve cell are generated. This include the production of neuroblasts and their differenciation into neurons. </YES> And this new "neurogenesis" term should be a "histogenesis".

<NO> [i]histogenesis ---[p]gliogenesis </NO>

gliogenesis is histogenesis, like neurogenesis. It is not part-of histogenesis.

Original comment by: lenov

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<YES> Counter proposal

Change term name:

neurogenesis ; GO:0007399

to:

nervous system development ; GO:0007399 def: The origin and formation of nervous tissue. broad_synonym: neurogenesis </YES> <YES> Add new term:

[i]nervous system development ; GO:0007399 ---[p]neurogenesis ; GO:new

neurogenesis ; GO:new def: The process by which nerve cell are generated. This include the production of neuroblasts and their differenciation into neurons. </YES> And this new "neurogenesis" term should be a "histogenesis".

<NO> [i]histogenesis ---[p]gliogenesis </NO>

gliogenesis is histogenesis, like neurogenesis. It is not part-of histogenesis.

Original comment by: lenov

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Hi,

Would these be reasonable definitions for the undefined terms?

gliogenesis ; GO:0042063 def: Morphogenesis of glial cells, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system.

glial growth ; GO:0042065 def: Growth of glial cells, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system.

Do you know how I should define this?

establishment of blood-nerve barrier ; GO:0008065

Thanks,

Jen

Original comment by: jenclark

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> nervous system development ; GO:0007399 > broad_synonym: neurogenesis and > neurogenesis ; GO:new

I must say, I've never been keen on using the same string as both a term name and a synonym (of any type/scope) for another term. We've actively avoided doing it elsewhere in the ontologies, and it would be best if we can come up with a way to avoid it for neurogenesis as well.

m

Original comment by: mah11

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I entirely agree. Suppress the synonym (that is wrong in addition)

Original comment by: lenov

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I just visited Nicolas and he also suggested this structure:

[i]histogenesis ; GO:0009888 ---[p]cell differentiation ; GO:0030154 ------[i]neuron differentiation ; GO:0030182 ------[i]glial cell differentiation ; GO:0010001 ---------[i]astrocyte differentiation ; GO:new ---------[i]oligodendrocyte differentiation ; GO:new ---------[i]microglia differentiation ; GO:new ---[i]neurogenesis ; GO:new ------[p]neuron differentiation ; GO:0030182 ---[i]gliogenesis ; GO:0042063 ------[p]glial cell differentiation ; GO:0010001 ------[i]astrocyte development ; GO:new ---------[p]astrocyte differentiation ; GO:new ------[i]oligodendrocyte development ; GO:new ---------[p]oligodendrocyte differentiation ; GO:new ------[i]microglia development ; GO:new ---------[p]microglia differentiation ; GO:new

This involves moving the high level term cell differentiation so we need to have a chat about that.

Jen

Original comment by: jenclark

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Further comment on neurogenesis from David:

I also think that neuron differentiation, neuron migration and all of the neuroblast terms should be made a part of neurogenesis (according to our new def of neurogenesis). Doug, do you agree with this?

David

Yes, this seems reasonable with the new def. of neurogenesis.

Doug

Original comment by: jenclark

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The neurogenesis def has previously been implemented and those child terms have now been moved.

I've implemented these defs since nobody objected:

gliogenesis ; GO:0042063 def: Morphogenesis of glial cells, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system.

glial growth ; GO:0042065 def: Growth of glial cells, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system.

Do you know how I should define this?

establishment of blood-nerve barrier ; GO:0008065

Does anybody have views on Nicholas's suggested structure of Date: 2005-09-06 09:33

Thanks,

Jen

Original comment by: jenclark

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Jen, Sorry to chime in late here..I must have lost track of this one in the email flood.

One question about the following: gliogenesis ; GO:0042063 def: Morphogenesis of glial cells, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system.

The def sounds more like 'glial morphogenesis', which relates to the generation of glial form rather than 'gliogenesis', which relates to the production of glial cells. 'gliogenesis' should be the glial version of 'neurogenesis', which is defined as "The process by which nerve cells are generated. This includes the production of neuroblasts and their differentiation into neurons. -Doug

Original comment by: doughowe

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D'y want to tell me exactly how you want it defined and I'll make the change?

Thanks,

Jen

Original comment by: jenclark

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How about:

gliogenesis: def: The process by which glial cells are generated. This includes the production of glial progenitors and their differentiation into mature glia.

Thx- -Doug

Original comment by: doughowe

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That's done now. Thanks Doug.

What do you all think about this suggestion from Nicholas?

[i]histogenesis ; GO:0009888 ---[p]cell differentiation ; GO:0030154 ------[i]neuron differentiation ; GO:0030182 ------[i]glial cell differentiation ; GO:0010001 ---------[i]astrocyte differentiation ; GO:new ---------[i]oligodendrocyte differentiation ; GO:new ---------[i]microglia differentiation ; GO:new ---[i]neurogenesis ; GO:new ------[p]neuron differentiation ; GO:0030182 ---[i]gliogenesis ; GO:0042063 ------[p]glial cell differentiation ; GO:0010001 ------[i]astrocyte development ; GO:new ---------[p]astrocyte differentiation ; GO:new ------[i]oligodendrocyte development ; GO:new ---------[p]oligodendrocyte differentiation ; GO:new ------[i]microglia development ; GO:new ---------[p]microglia differentiation ; GO:new

It's the last unresolved part of this sourceforge item.

Thanks,

Jen

Original comment by: jenclark

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In both the CNS and the PNS, there are many examples where neurons and glia develop from a common neuroglial precursor cell. If a gene is involved in the formation or developoment of this neuroglial precursor cell, where would we annotate it...concurrent annotations on 'neurogenesis' and 'gliogenesis'?

Some of this has already been edited, so I've updated the term names and added the IDs for existing terms below for further consideration.

i]tissue development; GO:0009888 <-renamed from histogenesis ---[p]cell differentiation ; GO:0030154 ------[i]neuron differentiation ; GO:0030182 ------[i]glial cell differentiation ; GO:0010001 ---------[i]astrocyte differentiation ; GO:0048708 ---------[i]oligodendrocyte differentiation ; GO:0048709 ---------[i]microglia differentiation ; GO:new ---[i]neurogenesis ; GO:0048699 ------[p]neuron differentiation ; GO:0030182 ---[i]gliogenesis ; GO:0042063 ------[p]glial cell differentiation ; GO:0010001 ------[i]astrocyte development ; GO:new ---------[p]astrocyte differentiation ; GO:new ------[i]oligodendrocyte development ; GO:new ---------[p]oligodendrocyte differentiation ; GO:new ------[i]microglia development ; GO:new ---------[p]microglia differentiation ; GO:new

Original comment by: doughowe

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In both the CNS and the PNS, there are many examples where neurons and glia develop from a common neuroglial precursor cell. If a gene is involved in the formation or developoment of this neuroglial precursor cell, where would we annotate it...concurrent annotations on 'neurogenesis' and 'gliogenesis'?

>>I would vote for the concurrent annotations. The problem here is that you want to include lineage in the annotation and it is a very slippery slope. Another solution would be to have the differentiation of a neuroglial precursor cell (perhaps the neuronal stem cell in the cell type ontology?)as a process and annotate to it. Then in the cell type ontology, both neurons and glia would develop from this cell type.

We also cannot put cell differentiation directly under tissue development. There are cells that differentiate and are not part of tissues. Perhaps it would work to make a term called "nervous tissue development" and have neurogenesis and gliogenesis be part_of children of it.

Also note that the term x-cell development in the GO does not mean the same thing as all developmental processes that have to do with an x-cell. It specifically means the development of the cell from when it starts to exist (after commitment) to the end of its life. This is not a perfect solution because it is not always the way people think about it but it means your graph should look like:

---[i]gliogenesis ; GO:0042063 ------[p]glial cell differentiation ; GO:0010001 --------[i]astrocyte differentiation ; GO:new -----------[p]astrocyte development ; GO:new --------[i]oligodendrocyte differentiation ; GO:new -----------[p]oligodendrocyte development ; GO:new --------[i]microglia differentiation ; GO:new --------- [p]microglia development ; GO:new

Cheers,

David

Original comment by: ukemi

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I will implement David's comment of Date: 2005-12-06 20:07 by the end of the week if nobody objects.

Thanks,

Jen

Original comment by: jenclark

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Erika is going to have a go at implementing David's comment of Date: 2005-12-06 20:07

Jen

Original comment by: jenclark

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Added new terms:

id: GO:0014002 name: astrocyte development namespace: biological_process def: "The process whose specific outcome is the progression of the astrocyte over time\, from its formation to the mature structure. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function." [GOC:ef] relationship: part_of GO:0048708 ! astrocyte differentiation

id: GO:0014003 name: oligodendrocyte development namespace: biological_process def: "The process whose specific outcome is the progression of the oligondendrocyte over time\, from its formation to the mature structure. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system." [GOC:ef] relationship: part_of GO:0048709 ! oligodendrocyte differentiation

[Term] id: GO:0014004 name: microglia differentiation namespace: biological_process def: "The process whereby a relatively unspecialized cell acquires specialized features of a microglial cell. Microglia are glial cells that act as the immune cells of the central nervous system. They form part of the supporting structure of this system." [GOC:ef] exact_synonym: "microglial cell differentiation" [] is_a: GO:0010001 ! glial cell differentiation

[Term] id: GO:0014005 name: microglia development namespace: biological_process def: "The process whose specific outcome is the progression of the microglial cell over time\, from its formation to the mature structure. " [GOC:ef] exact_synonym: "microglial cell development" [] relationship: part_of GO:0014004 ! microglia differentiation

Erika

Original comment by: arike

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I am moving this to a lower priority as it is not holiding back annotation.

Jen

Original comment by: jenclark

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• priority: 5 --> 3

Original comment by: jenclark

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Hi, I have added these terms:

id: GO:0014006 name: regulation of microglia differentiation namespace: biological_process def: "Any process that modulates the frequency\, rate or extent of microglia differentiation\, the process whereby a relatively unspecialized cell acquires specialized features of a microglial cell." [GOC:ef] exact_synonym: "regulation of microglial cell differentiation" [] is_a: GO:0045685 ! regulation of glial cell differentiation relationship: part_of GO:0014004 ! microglia differentiation

[Term] id: GO:0014007 name: negative regulation of microglia differentiation namespace: biological_process def: "Any process that stops\, prevents or reduces the frequency\, rate or extent of microglia differentiation\, the process whereby a relatively unspecialized cell acquires specialized features of a microglial cell." [GOC:ef] exact_synonym: "negative regulation of microglial cell differentiation" [] is_a: GO:0014006 ! regulation of microglia differentiation is_a: GO:0045686 ! negative regulation of glial cell differentiation

[Term] id: GO:0014008 name: positive regulation of microglia differentiation namespace: biological_process def: "Any process that activates\, maintains or increases the frequency\, rate or extent of microglia differentiation\, the process whereby a relatively unspecialized cell acquires specialized features of a microglial cell." [GOC:ef] exact_synonym: "positive regulation of microglial cell differentiation" [] is_a: GO:0014006 ! regulation of microglia differentiation is_a: GO:0045687 ! positive regulation of glial cell differentiation

Erika

Original comment by: arike

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I think the vast majority of the work proposed in this item has been done. While looking it over, I noticed that we left out my favorite glial cells of all..the Schwann cells. Also we did not relate specific instances of glial cell differentiation (like 'oligodendrocyte differentiation') to CNS or PNS development.

The solution:

I. Add new terms for Schwann cells as follows:

glial cell differentiation (GO:0010001) ---[i]Schwann cell differentiation (GO:new) ------[p]regulation of Schwann cell differentiation (GO:new) --------[i]positive regulation of Schwann cell differentiation (GO:new) --------[i]negative regulation of Schwann cell differentiation (GO:new) ------[p]Schwann cell development (GO:new)

peripheral nervous system development (GO:0007422) ---[p]Schwann cell differentiation (GO:new)

II. Add new relationships as follows

central nervous system development (GO:0007417) ---[p]oligodendrocyte differentiation (GO:0048709) ---[p]astrocyte differentiation (GO:0048708) ---[p]microglia differentiation (GO:0014004)

###################### Defs for new terms: All defs were made up by me.

Schwann cell differentiation: The process whereby a relatively unspecialized cell acquires the specialized features of a Schwann cell. Schwann cells are found in the peripheral

nervous system, where they insulate neurons and axons, and regulate the environment in which neurons function.

Schwann cell development: The process whose specific outcome is the progression of a Schwann cell over time, from its formation to the mature cell type. Schwann cells are

found in the peripheral nervous system, where they insulate neurons and axons, and regulate the environment in which neurons function.

regulation of Schwann cell differentiation: Any process that modulates the frequency, rate or extent of Schwann cell differentiation

positive regulation of Schwann cell differentiation: Any process that activates or increases the rate, frequency or extent of Schwann cell differentiation.

negative regulation of Schwann cell differentiation: Any process that stops, prevents or reduces the rate, frequency or extent of Schwann cell differentiation.

Original comment by: doughowe

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Hi Doug,

I am sorry that we have forgotten your "favorite" cells :-) I have a look of your terms and then I will implement them. Thanks Erika

Original comment by: arike

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Hi Doug, I have two questions:

1)Could we used the standard definition of Development instead of your definition? Standard development definition: the process aimed at the progression of a y cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.

2)In Go, there is a morpphogenesis term between development and cell differentiation. Would you like to have this type of term or not?

Thanks Erika

Original comment by: arike

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Hi all, I have added these terms. Thanks, Erika

[Term] id: GO:0014037 name: Schwann cell differentiation namespace: biological_process def: "The process whereby a relatively unspecialized cell acquires the specialized features of a Schwann cell. Schwann cells are found in the peripheral nervous system\, where they ins ulate neurons and axons\, and regulate the environment in which neurons function." [GOC:ef] is_a: GO:0010001 ! glial cell differentiation

[Term] id: GO:0014038 name: regulation of Schwann cell differentiation namespace: biological_process def: "Any process that modulates the frequency\, rate or extent of Schwann cell differentiation." [GOC:ef] is_a: GO:0045685 ! regulation of glial cell differentiation relationship: part_of GO:0014037 ! Schwann cell differentiation

[Term] id: GO:0014039 name: negative regulation of Schwann cell differentiation namespace: biological_process def: "Any process that stops\, prevents or reduces the rate\, frequency or extent of Schwann cell differentiation." [GOC:ef] is_a: GO:0014038 ! regulation of Schwann cell differentiation is_a: GO:0045686 ! negative regulation of glial cell differentiation

[Term] id: GO:0014040 name: positive regulation of Schwann cell differentiation namespace: biological_process def: "Any process that activates or increases the rate\, frequency or extent of Schwann cell differentiation." [GOC:ef] is_a: GO:0014038 ! regulation of Schwann cell differentiation is_a: GO:0045687 ! positive regulation of glial cell differentiation

Original comment by: arike

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Yes, please use the std. def. like this:

Schwann cell development: The process aimed at the progression of a Schwann cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.

Regarding your second question, the std. structure for development involving cells would produce somthing like this I think:

glial cell differentiation [i] Schwann cell differentiation ---[p] Schwann cell fate commitment ------[p] Schwann cell fate specification ------[p] Schwann cell fate determination ---[p] Schwann cell development ------[i] cellular morphogenesis during Schwann cell differentiation ------[i] Schwann cell maturation

With additional relationships to terms like "glial cell fate determination". I don't see the morphogenesis term you were asking about, but I see a few additional terms that weren't included in my original Schwann cell request.

You might ask Jen &/or David what there thoughts are on how complete we should be when following the standard structures under the Development node. This area produces ALOT of terms and relationships.

-Doug

Original comment by: doughowe

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You might ask Jen &/or David what there thoughts are on how complete we should be when following the standard structures under the Development node. This area produces ALOT of terms and relationships.

We can do it now, or we can do it later. They should all be valid terms.

David

Original comment by: ukemi

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Hi Doug, I am sorry, my question about morphonogenesis refered to these terms: central nervous system development (GO:0007417) ---[p]oligodendrocyte differentiation (GO:0048709) ---[p]astrocyte differentiation (GO:0048708) ---[p]microglia differentiation (GO:0014004)

The standard structure for development is:

x development [p] x morphogenesis ---[p] x formation ------[p] y cell differentiation ---[p] x structural organisation [p] x maturation

So do you want some terms as children of central nervos system development. The problem is that we have a term "central nervous system development" that refers to a system and children terms oligodendrocyte differentiation, astrocyte differentiation, microglia differentiation that refer to cell. Does exist a term that refer to a tissue to put in the stRucture?

Thanks Erika

Original comment by: arike

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Hi, I have added this term: [Term] id: GO:0014044 name: Schwann cell development namespace: biological_process def: "The process whose specific outcome is the progression of a Schwann cell over time, from its formation to the mature cell type. Schwann cells are found in the peripheral ner vous system, where they insulate neurons and axons, and regulate the environment in which neurons function." [GOC:ef] relationship: part_of GO:0014037 ! Schwann cell differentiation

Thanks

Erika

Original comment by: arike

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Hmm....this is a tough one. We do have the term 'brain development' as a child of 'central nervous system' development. 'brain development' could serve as the tissue you are looking for. However, the glial cells that are the children we are dealing with also occur in the spinal cord, which is also part of the central nervous system.

This might mean we would need terms like 'brain astroctye differentiation' and 'spinal cord astrocyte differentiation' to be children of 'brain development' and 'spinal cord development' respectively..?

To avoid overcomplicating things at this stage, maybe it is OK to have the various glial cell differentiation terms as direct children of the 'central nervous system development'. This is biologically correct, though perhaps not ontologically complete.

One could possibly make the argument that despite their names, the 'central nervous system' and the 'peripheral nervous system' are kind of "organy" systems that are a part of the bona fide system we call the 'nervous system'?

-Doug

Original comment by: doughowe

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I found a couple of relationships here to "neurogenesis" terms that can be removed now that 'neurogenesis' is being used to refer solely to neurons. The new parents should reflect "gliogenesis" instead.

I. 'regulation of neurogenesis' (GO:0050768) ---'regulation of glial cell differentiation'(GO:0045686)

Should be changed to:

'regulation of gliogenesis'(GO:0014013) ---'regulation of glial cell differentiation'(GO:0045686)

II. 'positive regulation of neurogenesis' (GO:0050769) ---'positive regulation of glial cell differentiation'(GO:0045687)

Should be changed to:

'positive regulation of gliogenesis' (GO:0014015) ---'positive regulation of glial cell differentiation'(GO:0045687)

Thanks! -Doug

Original comment by: doughowe

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Dear Doug, My thought was the same of yours. But I asked comments for being sure. I think that you could consider "nervous system" as a kind of organ for not complicating the ontology. So, I will implement these terms and i Will change the positions of the other terms about glial cells.

Thnak you Erika

Original comment by: arike

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Hi, I have fixed relationships of terms about gliogenesis (GO:0042063) and glial cell differentiation (GO:0010001). See the comment Date: 2006-02-20 21:40 and Date: 2006-02-15 00:51.

Thanks Erika

Original comment by: arike

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I think a few cell development terms got the std. def intended for structure development terms by accident. I've provided the following defs to use the std cell development format.

The defs should change to:

'astrocyte development' GO:0014002 The process aimed at the progression of an astrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function.

'microglia development' GO:0014005 The process aimed at the progression of a microglial cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.

'oligodendrocyte development' GO:0014003 The process aimed at the progression of an oligodendrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. An oligodendrocyte is a type of glial cell involved in myelinating the axons in the central nervous system.

'Schwann cell development' GO:0014044 The process aimed at the progression of a Schwann cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. Schwann cells are found in the peripheral nervous system, where they insulate neurons and axons, and regulate the environment in which neurons function.

-Doug

Original comment by: doughowe

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I think burried in this SF request somewhere was a plea for a definition of "establishment of blood-nerve barrier" GO:0008065.

So here ya go: Term string should be changed to "establishment of blood-brain barrier". The current "blood-nerve" verbiage could be retained as a synonym..but I've never heard it called that.

Definition: Establishment of the endothelial barrier between the blood and the brain. The endothelial cells in the brain capillaries are packed tightly together preventing the passage of most molecules from the blood into the brain. Only lipid soluble molecules or those which are actively transported can pass through the blood-brain barrier.

dbxref = me

-Doug

Original comment by: doughowe