neuroblast specification

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Hi all! I would like to suggest a new term. neuroblast cell specification

The DAG strucuture could be:

[i]neurogenesis;GO:0048699 ---[p]neuroblast specification;GO:new

Def: Process wherein cells that have been activated to become neuroblast, can enter the neural differentiation pathway but the progression along this pathway can be repressed by presence of neural inhibitory signals. So, the cells fate can be reversed.

Ref: ISBN: 0878932585, PMID: 11687825

thank you Erika

Reported by: arike

Original Ticket: "geneontology/ontology-requests/3145":https://sourceforge.net/p/geneontology/ontology-requests/3145

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Erika,

I am fine with this term, but we should put it in the correct context of cell differentiation.

neuroblast differentiation %cell differentiation --<neuroblast fate commitment ----<neuroblast fate specification ----<neuroblast fate determination ; GO:000740 --<neuroblast development

At some point most of the terms that contain neuroblast should be related to these. Are you a neurobiologist? If so, do you think that a neuroblast and a neuronal precursor cell are the same thing? I have niticed that when people talk about neuronal cells migrating through the cerebral cortex, they always call them neuronal precursors.

David

Original comment by: ukemi

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Hi David,

I am sorry but I am not a neurobiologist. I am interested on it and I am trying to enrich my knownledge about it.

Neuroblast definition: Cells arising by division of precursor cells in neural ectoderm (neurectoderm) that subsequently differentiate to become neurons (http://cancerweb.ncl.ac.uk/cgi-bin/omd?neuroblast ).So, for me a neuroblast is a 'dividing neuronal precursor cell'. Is it correct?

The cell differentiation could be the proper parent term for new terms about "neuroblast" but I think that we could add these new terms as a part-of children of both neurogenesis and cell differentiation. What do you think? Erika

Original comment by: arike

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/The cell differentiation could be the proper /parent term for new terms about "neuroblast" but I /think that we could add these new terms as a /part-of children of both neurogenesis and cell /differentiation. What do you think?

It certainly could be a part of neurogenesis. I would suggets

neurogenesis ; GO:0048699 --<neuroblast differentiation ; GO:new ----<neuroblast fate commitment ; GO:new ------<neuroblast fate specification ; GO:new ------<neuroblast fate determination ; GO:0007400 ----<neuroblast development ; GO:new

cell differentiation ; GO:0030154 --%neuroblast differentiation ; GO:new

cell development ; GO:0048468 --%neuroblast development ; GO:new

cell fate commitment ; GO:0045165 --%neuroblast fate commitment ; GO:new

cell fate specification ; GO:0001708 --%neuroblast fate specification ; GO:new

cell fate determination ; GO:0001709 --%neuroblast fate determination ; GO:0007400

/Neuroblast definition: Cells arising by division /of precursor cells in neural ectoderm /(neurectoderm) that subsequently differentiate to /become neurons /(http://cancerweb.ncl.ac.uk/cgi-bin/omd?neuroblast /).So, for me a neuroblast is a 'dividing neuronal /precursor cell'. Is it correct?

I'm not sure, that is why I was asking you. It just seems that when the cells are migrating in the cortex, they are always called neuronal precursors. I usually consider these as neuroblasts. But, if they are already committed to becoming neurons, then we should consider them neurons. From a GO perspective, a neuron begins to exists once it is committed to that fate.

David

Original comment by: ukemi

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so, let me see if I have understood the difference between neuroblast and neuronal precursor cell. Only when the fate of a neuroblast has been decided then it could became and it could be called a neuron. Is it correct? So the neural precursor cell is a cell at a lower level than a neuroblast level. Isn't it? Erika

Original comment by: arike

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That's just it. I'm not sure. I've been using neuronal precursor cell and neuroblast interchangeably. I would like to know if there is a difference.

David

Original comment by: ukemi

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Hi David,

I think that we can say that a neuroblast is a neuronal precursor cell. All the cells, starting from the neuroectodermcells until the neuroblast could be consider neuronal precursor cell.All cells before neron or glia could be considere neuro-glial cell precursor, aren't they? The problems is if a neuronal precursor cell is also a glia precursor cell or not! But in the Go we have already this distinction because we have gliogenesis and neurogenesis.

I have a proposal for you:

neuroblast differentiation Def: The process whereby a relatively unspecialized cell acquires specialized features of a neuroblast.There are at least four stages through which the pluripotent cells of epiblast or blastula become neural precursor cells, or neuroblasts.

neuroblast fate commitment Def: The process whereby the developmental fate of a cell becomes restricted such that it will develop into a neuroblast.

neuroblast fate specification Def: The process whereby a cell becomes capable of differentiating autonomously into a neuroblast in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed.

neuroblast development Def: The process whose specific outcome is the progression of a neuroblast over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.

neurogenesis ; GO:0048699 ---[i]neuroblast differentiation ; GO:new ------[p]neuroblast fate commitment ; GO:new ---------[p]neuroblast fate specification ; GO:new ---------[p]neuroblast fate determination ; GO:0007400 ------[p]neuroblast development ; GO:new ---[p]neuroblast activation ; GO:0007407 ---[p]neuroblast proliferation ; GO:0007405

cell differentiation ; GO:0030154 ---[i]neuroblast differentiation ; GO:new

---[p]cell development ; GO:0048468 ------[i]neuroblast development ; GO:new

---[p]cell fate commitment ; GO:0045165 ------[i]neuroblast fate commitment ; GO:new

---[p]cell fate specification ; GO:0001708 ------[i]neuroblast fate specification ; GO:new

What do you think? Erika

Original comment by: arike

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Hi Erika,

I agree with your proposed structure. I think for now the best thing to do with neuroblast and neuronal precursor is to consider them equivalent. Neuroblast proliferation should be an is_a cell proliferation as well.

David

Original comment by: ukemi

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I agree with David. For the time being, we should remain a little vague with respect to 'neuroblasts' vs. 'neuronal progenitors'. The literature is very unclear on the meaning of these words, and I think the biology is very diverse as well. It will be difficult to come up with a correct representation for GO.

Original comment by: doughowe

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The latest proposed defs may need some massaging. For example, I think a 'neuroblast' is a multi-potent cell capable of producing neuronal progenitor cells (cells that will become various types of neurons) as well as glial progenitor cells (cells that will become various types of glia).

Consequently, I'm not sure something like this will work:

" neuroblast development Def: The process whose specific outcome is the progression of a neuroblast over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. "

The biology gets very dirty very fast here...

Original comment by: doughowe

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Doug,

I think this def might be o.k. We made the decision a while ago that cell differentiation would not include lineage information. So neuroblast development would include the processes after a cell is committed to a neuroblast until it is a mature neuroblast.It would not include processes where the neuroblast turns into a glial cell or a neuron. The process where a neuroblast becomes committed to a glial cell and turns into a mature glial cell would be glial cell differentiation and likewise for a neuron it would be neuronal differentiation.

David

Original comment by: ukemi

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Just a quick addition. If in the cell type ontology we have the lineage relationships between cell types, then we can use this info to elaborate on the definitions of differentiation. So, we could include lineage info in the def, but it would not be represented in the process ontology per se.

David

Original comment by: ukemi

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Hi,

I agree with David about the definition of neuroblast, neuroblast development and neuronal differentiation. Sure, we could use the information in cell ontology to improve our definitions. I am looking for doing this. Erika

Original comment by: arike

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This structure should be OK then. -Doug

Original comment by: doughowe

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Hi, I have problems to find the definition of neuroblast in the cell ontology because there isn't a definition. The cell ontology confirm anly the thing that a neuroblast derives from neuroectoderms. I think that we could leave he idea of insert a lineage in the definition of the terms! What do ou think?

Erika

Original comment by: arike

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I agree. The lineage issue is very difficult. Even just defining 'neuroblast' is difficult. I think the proposed structure is OK. I've re-inserted it here to keep it near the top of the thread:

neurogenesis ; GO:0048699 ---[i]neuroblast differentiation ; GO:new ------[p]neuroblast fate commitment ; GO:new ---------[p]neuroblast fate specification ; GO:new ---------[p]neuroblast fate determination ; GO:0007400 ------[p]neuroblast development ; GO:new ---[p]neuroblast activation ; GO:0007407 ---[p]neuroblast proliferation ; GO:0007405

cell differentiation ; GO:0030154 ---[i]neuroblast differentiation ; GO:new

---[p]cell development ; GO:0048468 ------[i]neuroblast development ; GO:new

---[p]cell fate commitment ; GO:0045165 ------[i]neuroblast fate commitment ; GO:new

---[p]cell fate specification ; GO:0001708 ------[i]neuroblast fate specification ; GO:new

Original comment by: doughowe

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Hi all, this is the final structure with the definitions. If there are no problems, I will implement it on Thursday.

neurogenesis ; GO:0048699 ---[i]neuroblast differentiation ; GO:new ------[p]neuroblast fate commitment ; GO:new ---------[p]neuroblast fate specification ; GO:new ---------[p]neuroblast fate determination ; GO:0007400 ------[p]neuroblast development ; GO:new ---[p]neuroblast activation ; GO:0007407 ---[p]neuroblast proliferation ; GO:0007405

---cell differentiation ; GO:0030154 ---[i]neuroblast differentiation ; GO:new

---[p]cell development ; GO:0048468 ------[i]neuroblast development ; GO:new

---[p]cell fate commitment ; GO:0045165 ------[i]neuroblast fate commitment ; GO:new

---[p]cell fate specification ; GO:0001708 ------[i]neuroblast fate specification ; GO:new

---[i] cell proliferation ; GO:0008283 ------[p] neuroblast proliferation ; GO:new

neuroblast differentiation Def: The process whereby a relatively unspecialized cell acquires specialized features of a neuroblast.There are at least four stages through which the pluripotent cells of epiblast or blastula become neuroblasts.

neuroblast fate commitment Def: The process whereby the developmental fate of a cell becomes restricted such that it will differentiate into a neuroblast.

neuroblast fate specification Def: The process whereby a cell becomes capable of differentiating autonomously into a neuroblast in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed.

neuroblast fate specification ; GO: 007400 Def: The process by which a cell becomes capable of differentiating autonomously into a neuroblast cell regardless of its environment; upon determination, the cell fate cannot be reversed.

neuroblast development Def: The process aimed at the progression of a neuroblast over time, from initial commitment of the cell to a specific state, to the mature neuroblast. It does not include processes where the neuroblast turns into a glial cell or a neuron.

neuroblast proliferation Def: The multiplication or reproduction of neuroblasts, resulting in the rapid expansion of the population.

What do you think? Could be the DAG and definitions right?

Thank you Erika

Original comment by: arike

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• milestone: --> Plant Ontology
• priority: 5 --> 9
• assigned_to: nobody --> jenclark

Original comment by: jenclark

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This one is o.k. too.

David

Original comment by: ukemi

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Hi, I have added new terms:

id: GO:0014016 name: neuroblast differentiation namespace: biological_process def: "The process whereby a relatively unspecialized cell acquires specialized features of a neuroblast. There are at least four stages through which the pluripotent cells of epi blast or blastula become neuroblasts." [GOC:ef, ISBN:0878932585] is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0048699 ! neurogenesis

[Term] id: GO:0014017 name: neuroblast fate commitment namespace: biological_process def: "The process whereby the developmental fate of a cell becomes restricted such that it will differentiate into a neuroblast." [GOC:ef, ISBN:0878932585] is_a: GO:0045165 ! cell fate commitment relationship: part_of GO:0014016 ! neuroblast differentiation

[Term] id: GO:0014018 name: neuroblast fate specification namespace: biological_process def: "The process whereby a cell becomes capable of differentiating autonomously into a neuroblast in an environment that is neutral with respect to the developmental pathway. Up on specification\, the cell fate can be reversed." [GOC:ef, ISBN:0878932585] is_a: GO:0001708 ! cell fate specification relationship: part_of GO:0014017 ! neuroblast fate commitment

[Term] id: GO:0014019 name: neuroblast development namespace: biological_process def: "The process aimed at the progression of a neuroblast over time\, from initial commitment of the cell to a specific state\, to the mature neuroblast. It does not include pro cesses where the neuroblast turns into a glial cell or a neuron." [GOC:ef, ISBN:0878932585] is_a: GO:0048468 ! cell development relationship: part_of GO:0014016 ! neuroblast differentiation

Thanks, erika

Original comment by: arike

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• priority: 9 --> 5
• status: open --> closed-accepted

Original comment by: arike

[gocentral]

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

Original comment by: cooperl09