neuroblast division (sensu Vertebrata);GO:0043345

[gocentral]

This term does not seem right at all. I think it is a cse of getting carried away with standardized definitions. I have never heard of a GMC in vertebrate embryos. I also don't think that in vertebrates neuroblast division has anything to do with cell fate commitment of a neuroblast, it is just a way to make more neuroblasts. Does anyone know this off the top of their head before I dive deeper into it?

David

Reported by: ukemi

Original Ticket: "geneontology/ontology-requests/3171":https://sourceforge.net/p/geneontology/ontology-requests/3171

[gocentral]

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Gosh - this term is in my id range, but I have no memory of it at all. It's not the sort of term I'd normally get involved with, let me see if I can track down why I added it...

Original comment by: jl242

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Okay - it was added with a whole load of other terms as part of the CL-GO alignment which is why I didn't remember it - let me find the SF item...

Original comment by: jl242

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It's here:

https://sourceforge.net/tracker/?group\_id=36855&atid=440764&func=detail&aid=1192419

Original comment by: jl242

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I agree. As far as I can tell, GMCs are not found in vertebrates, and 'neuroblast division (sensu Vertebrate) should probably not be related to cell fate commitment.

PMID:12810590 says the following about neuroblast division in zebrafish:

"...we have determined that the majority of neurons in the zebrafish embryo hindbrain are born from progenitor divisions that generate two neurons. Divisions that generate a progenitor as well as a neuron do occur, but they represent only 17% of the progenitor divisions monitored and many of these asymmetric divisions appear to be restricted to a particular generation within a family tree."

Original comment by: doughowe

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I guess this is going to be obsoleted. Jane do you want to do it or shall I?

Jen

Original comment by: jenclark

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presumably this term is still on the chopping block after the CNS revisions ... shall I send an obsoletion-announcement email?

m (since everyone else is busy)

Original comment by: mah11

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I'm all for either obsoleting it or merging it into its parent. The parent is also not defined correctly. It seems that the parent is defined by the invertebrate example. The parent should simply be the division of a neuroblast.

[Term] id: GO:0045034 name: neuroblast division namespace: biological_process def: "The processes resulting in the physical partitioning and separation of a neuroblast into daughter cells." [GO:curators] is_a: GO:0051301 ! cell division relationship: part_of GO:0007405 ! neuroblast proliferation

[Term] id: GO:new name: symmetric neuroblast division namespace: biological_process def: "The processes resulting in the physical partitioning and separation of a neuroblast into two equi-potent daughter cells." [GO:curators] is_a: GO:0045034 ! neuroblast division relationship: part_of GO:0007405 ! neuroblast proliferation

[Term] id: GO:new name: asymmetric neuroblast division namespace: biological_process def: "The processes resulting in the physical partitioning and separation of a neuroblast into two daughter cells with different developmental potentials." [GO:curators] is_a: GO:0045034 ! neuroblast division is_a: GO:0008356 ! asymmetric cell division relationship: part_of GO:0022008 ! neurogenesis

[Term] id: GO:0043346 name: asymmetric neuroblast division resulting in ganglion mother cell formation namespace: biological_process def: "The processes resulting in the physical partitioning and separation of a neuroblast into a neuroblast and a ganglion mother cell." [GO:curators] is_a: GO:new ! asymmetric neuroblast division relationship: part_of GO:0022008 ! neurogenesis

Unless this division is really an integral part of the fate determination of either the neuroblast or the ganglion mother cell, I would remove the link to fate determination. Perhaps a part of the asymmetric division, such as the segregaton of cytoplasmic components is responsible for the fate decisions. If this is true, then this should be a part of the fate determination and a part of the asymmetric division.

David

Original comment by: ukemi

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I like David's new terms and defs., and I like getting rid of the sensu. -Doug

Original comment by: doughowe

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fine by me too; who wants to implement? m

Original comment by: mah11

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I think it might as well be implemented with the rest of the nervous system stuff.

David

Original comment by: ukemi

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I guess that means you, Jen -- OK?

(holler if you need help) m

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> ukemi

Original comment by: mah11

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Hi David,

This is assigned to you. Do you want to do the implementation or shall I?

Jen

Original comment by: jenclark

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Jen,

This was just assigned to me a few minutes ago. I think it was addressed during the neuro meeting, but I was going to check. If you are editing and it is straightforward, go ahead and take it. If there are any questions, let me know and I'll deal with it. Or, if you just want me to implement, I can do that too.

David

Original comment by: ukemi

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Hi David,

I'm a bit snowed under just now with transport and sensu and the outreach group so if you can implement that would be great. If not you could leave it on my to do pile.

Thanks,

Jen

Original comment by: jenclark

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That's fine. If I do it, I'll close it. If not it will stay open. I plan to do it.

David

Original comment by: ukemi

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Great. If I find myself at a loose end I'll also consider this item fair game for implementation.

I guess this is what they mean by triage then. Just a thought, but in my list I usually put items like this to the highest priority so they're easy to spot in a spare moment. It turns the items to a darker colour in the list.

Jen

Original comment by: jenclark

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Hi--

We've been discussing the neuroblast division terms at WormBase and so I thought I'd pass along our comments.

Any cells described as neuroblasts in the C. elegans literature undergo asymmetric divisions as far as we know. Having said that, however, we are not certain that cells described as neuroblasts in C. elegans fit the definition of neuroblast in the cell type ontology. Namely, elegans "neuroblasts" don't behave like stem cells. They don't maintain the ability to divide and renew throughout the worm's life cycle.

So, if the definition of neuroblast in these GO terms is that stated in the cell type ontology, then we probably couldn't annotate to them. We would either have to annotate to other terms or suggest related nematode-specific terms.
We'd have to look into that further to see what would be more appropriate.

--Kimberly

Original comment by: vanaukenk

[gocentral]

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Kimberly,

Thanks for your comments! I think that I am going to opt for an obsoletion of the neuroblast division term and a reconstruction of this part of the graph. I could not see that 'neuroblast' is defined in the cell ontology, so I'm wondering where you got the definition. I don't think the definition fits for mammals either where there are several kinds of neuroblasts, including radial glial cells that give rise to neurons and glia. I think that 'neuroblast' is used to represent any kind of precursor cell that will divide and give rise to a neuron. Does this fit with your view? We can work with the cell type ontology. They have been very responsive to our queries and additions. I think the definition of 'neuroblast differentiation' in the GO is open enough that it works. I might add a sentence that says "A neuroblast is any cell that will divide and give rise to a neuron". For the neuroblast division terms, I will probaly create the terms that are specified earlier in this thread.

[Term] id: GO:new name: neuroblast division namespace: biological_process def: "The processes resulting in the physical partitioning and separation of a neuroblast into daughter cells. A neuroblast is any cell that will divide and give rise to a neuron" [GO:curators] is_a: GO:0051301 ! cell division relationship: part_of GO:0007405 ! neuroblast proliferation

[Term] id: GO:new name: symmetric neuroblast division namespace: biological_process def: "The processes resulting in the physical partitioning and separation of a neuroblast into two equi-potent daughter cells." [GO:curators] is_a: GO:0045034 ! neuroblast division relationship: part_of GO:0007405 ! neuroblast proliferation

[Term] id: GO:new name: asymmetric neuroblast division namespace: biological_process def: "The processes resulting in the physical partitioning and separation of a neuroblast into two daughter cells with different developmental potentials." [GO:curators] is_a: GO:0045034 ! neuroblast division is_a: GO:0008356 ! asymmetric cell division relationship: part_of GO:0022008 ! neurogenesis

[Term] id: GO:New name: asymmetric neuroblast division resulting in ganglion mother cell formation namespace: biological_process def: "The processes resulting in the physical partitioning and separation of a neuroblast into a neuroblast and a ganglion mother cell." [GO:curators] is_a: GO:new ! asymmetric neuroblast division relationship: part_of GO:0022008 ! neurogenesis

Would this work for you guys??

David

Original comment by: ukemi

[gocentral]

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Hi David--

You're right about the cell type ontology not having a definition for neuroblast. I got the idea about a neuroblast being self-renewing from tracing the term neuroblast (using is_a relationships) back to the parent term, stem cell. Is that the relationship that you see, too?

If we instead define neuroblast as any precursor cell that will divide and give rise to a neuron, that would be completely consistent with how the term is used in the elegans literature and we could definitely annotate to these new neuroblast terms.

So, it looks like the definition of neuroblast is the only thing we need to settle on.

Thanks, Kimberly

Original comment by: vanaukenk

[gocentral]

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This is great! I had forgotten about this case.

Shall we also recommend then that the CL ontology merge these three: 'neuroblast' (CL:0000031) 'neuroblast (sensu vertebrata)'(CL:0000337) 'neuroblast (sensu nematoda and protostomia)' CL:0000338 ?

Also, CL has a term 'neuroglioblast', under which falls 'ganglion mother cell'

GO will either need terms like 'neuroglioblast division', or CL will need to lose it's 'neuroglioblast' cell type I think? -Doug

Original comment by: doughowe

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I think the following might be good for the CL 'neuroblast' terms?:

merge: CNS neuron (sensu vert) CL:117 CNS neuron (sensu nematod and protostom) CL:28 and rename to 'CNS neuron'

merge: 'neuroblast (sensu vert)' CL:338 'neuroblast (sensu nematod & protostom)' CL:337 'neuroglioblast' CL:468 'neuroglioblast (sensu nematod) CL:662 and rename to 'neuroblast'

---

After that, the CL term 'ganglion mother cell' will be is_a 'neuroblast', which seems OK.

-Doug

Original comment by: doughowe

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Jen and David obsoleted the old neuroblast division term and merged the sensu terms. Added:

neuroblast division ; GO:0055057 symmetric neuroblast division ; GO:0055058 asymmetric neuroblast division ; GO:0055059 asymmetric neuroblast division resulting in ganglion mother cell formation ; GO:0055060

Original comment by: ukemi

[gocentral]

• status: open --> closed

Original comment by: ukemi