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segment-specific terms for VNC/GG neuroblasts #1179

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Clare72 opened this issue Jun 11, 2021 · 2 comments · Fixed by #1554
Closed

segment-specific terms for VNC/GG neuroblasts #1179

Clare72 opened this issue Jun 11, 2021 · 2 comments · Fixed by #1554
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new term request new terms needed tricky non-standard issue that may require extra thought/research VFB related to the nervous system/requested by VFB

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@Clare72
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Clare72 commented Jun 11, 2021

There is mostly complete information about which VNC/GG neuroblasts are present in which segments in the following papers:
Urbach et al. (2016) - FBrf0232096
Birkholz et al. (2013) - FBrf0221210

Details of which NBs produce a secondary lineage in:
Lacin and Truman, (2016) (fig1s1) - FBrf0231327
(but probably not relevant to this issue)

There are enough differences between segments, such as whether a seconday lineage is produced, delamination window and gene expression, that it is probably worth having the specifc terms rather than using the parent terms for all segments.

Can also add GCIs for autoclassification, but would need a lot of GCIs (for each neuroblast-neuromere combination)...

neuron that develops from some [NB] and has soma location some [neuromere] SubClassOf neuron that develops from some ([NB] and part_of some [neuromere])

Otherwise, may have to manually assert segment-specific neuroblasts for segment-specific neuron classes

@Clare72 Clare72 added new term request new terms needed VFB related to the nervous system/requested by VFB tricky non-standard issue that may require extra thought/research labels Jun 11, 2021
@Clare72 Clare72 self-assigned this Jun 11, 2021
@Clare72
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Clare72 commented Jun 16, 2021

We may be able to use one term to cover A1-7 (similar to motor neurons), though I am not a huge fan of the A1-7 MN terms, but gnathal, thoracic and terminal neuroblasts should probably have specific terms.

Rather than adding loads of GCIs, we could make neuromere-specific lineage terms:
'[neuromere] lineage [neuroblast] neuron' == neuron that develops_from some [neuroblast] and has_soma_location some [neuromere]

SC develops_from some ([neuroblast] that part_of some [neuromere])

@Clare72
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Clare72 commented Nov 1, 2022

see also FBrf0231386 and FBrf0238045 for gnathal neuroblasts

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new term request new terms needed tricky non-standard issue that may require extra thought/research VFB related to the nervous system/requested by VFB
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