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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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neuron develops-from some vertebrate neuroblast leads to incoherency #757

Closed cmungall closed 4 years ago

cmungall commented 4 years ago

image

cmungall commented 4 years ago

neuron-develops-from-vertebrate neuroblast is the issue

Note this unsat only arises on my branch where I am bringing in uberon TCs (for #709)

cmungall commented 4 years ago

Side issue for @balhoff

this makes the TC plugin do weird stuff

image

branch issue-709-uberon-base to replicate

cmungall commented 4 years ago

@dosumis you know most about difference in usage of 'neuroblast' across metazoa, can you recommend action?

We could simply have a GCI, neuron and in some Vert Sub dev-from some Vert neuroblast. But I'd like to pick more at the modeling here:

currently the "nematode and protostome" neuroblast (is this even a meaningful grouping?) has no texture definition. It is a neuronal stem cell (correct)

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(suspiciously, the only subclasses of neuronal stem cell are nemo-proto)

in verts it has a definition, but not a stem cell (correct), it's non-terminally differentiated (correct), but is incomplete - no develops-from asserted or inferred:

image

I don't think any of this is wrong, it just seems suboptimal modeling

in fbbt the genus is neural stem cell though this is not a distinct concept:

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in wbbt it's a blast cell. Not sure enough of c elegans development to say if this inconsistent with calling it

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None of this is actually wrong, but it seems confusing and incomplete

in verts we presumably want to trace a lineage neuron back to neural stem cells, e.g. via RG cells

cmungall commented 4 years ago

going with a GCI, which is not wrong:

![Uploading image.png…]()

dosumis commented 4 years ago

GCI is fine. Discussion of why we need separate sensu terms for vertebrate and invertebrate neuroblasts is here: https://github.com/obophenotype/cell-ontology/issues/617#issuecomment-580862253

in fbbt the genus is neural stem cell though this is not a distinct concept:

Not needed as neuroblasts are the only neural stem cells in flies (probably true in all arthropods). I have no idea about nematodes.

Looks to me like radial glia should go under neural stem cell:

"During the late stages of neurogenesis, radial glial cells divide asymmetrically in the ventricular zone, generating a new radial glial cell, as well as a postmitotic neuron or an intermediate progenitor (IPC) daughter cell" https://en.wikipedia.org/wiki/Radial_glial_cell#Progenitors

Don't know whether all vertebrate neuroblasts develop from radial glia though.

balhoff commented 4 years ago

This issue is preventing import of cl-base into GO.

matentzn commented 4 years ago

If someone fixes it I can immediately run a new release.

cmungall commented 4 years ago

@matentzn - as soon as the PR check completes successfully, merge and make a new release, thanks!