Where are all the cerebellar cortex neurons in the CUTs

[memartone]

I only see two. Purkinje cell is missing and all the other well known cell types.

[tgbugs]

hasPhenotype some (cerebellum or ('part of' some cerebellum)) returns 10 results for me.

'Mammalia cerebellar nuclear complex interneuron'
'Mammalia cerebellar nuclear complex projection neuron'
'Mammalia cerebellum (unionOf granular layer of cerebellar cortex Purkinje cell layer of cerebellar cortex) +GABA neuron'
'Mammalia cerebellum molecular layer of cerebellar cortex (with-axon-in molecular layer of cerebellar cortex) Stellate +GABA neuron'
'Mammalia granular layer of cerebellar cortex (with-axon-in granular layer of cerebellar cortex) +CR +Glu interneuron'
'Mammalia granular layer of cerebellar cortex (with-axon-in granular layer of cerebellar cortex) +GABA neuron'
'Mammalia granular layer of cerebellar cortex (with-axon-in molecular layer of cerebellar cortex) +GluR +Glu neuron'
'Mammalia molecular layer of cerebellar cortex (with-axon-in Purkinje cell layer of cerebellar cortex) Basket +GABA interneuron'
'Mammalia Purkinje cell layer of cerebellar cortex (with-axons-in cerebellar nuclear complex Purkinje cell layer of cerebellar cortex) +AMPA +GABA-gated anionic channel +GABA projection neuron'
'Mammalia Rodent cerebellum Purkinje cell layer of cerebellar cortex neuron'

and 'Mammalia Purkinje cell layer of cerebellar cortex (with-axons-in cerebellar nuclear complex Purkinje cell layer of cerebellar cortex) +AMPA +GABA-gated anionic channel +GABA projection neuron' has origLabel "Cerebellum Purkinje cell"

[memartone]

I think I got fooled by this before. In my view, since granular cell layer is a layer, then it is no different than neocortex layer 2/3, so should be cerebellar cortex Purkinje cell layer...

On Jun 15, 2019, at 9:24 PM, Tom Gillespie notifications@github.com wrote:

hasPhenotype some (cerebellum or ('part of' some cerebellum)) returns 10 results for me.

'Mammalia cerebellar nuclear complex interneuron' 'Mammalia cerebellar nuclear complex projection neuron' 'Mammalia cerebellum (unionOf granular layer of cerebellar cortex Purkinje cell layer of cerebellar cortex) +GABA neuron' 'Mammalia cerebellum molecular layer of cerebellar cortex (with-axon-in molecular layer of cerebellar cortex) Stellate +GABA neuron' 'Mammalia granular layer of cerebellar cortex (with-axon-in granular layer of cerebellar cortex) +CR +Glu interneuron' 'Mammalia granular layer of cerebellar cortex (with-axon-in granular layer of cerebellar cortex) +GABA neuron' 'Mammalia granular layer of cerebellar cortex (with-axon-in molecular layer of cerebellar cortex) +GluR +Glu neuron' 'Mammalia molecular layer of cerebellar cortex (with-axon-in Purkinje cell layer of cerebellar cortex) Basket +GABA interneuron' 'Mammalia Purkinje cell layer of cerebellar cortex (with-axons-in cerebellar nuclear complex Purkinje cell layer of cerebellar cortex) +AMPA +GABA-gated anionic channel +GABA projection neuron' 'Mammalia Rodent cerebellum Purkinje cell layer of cerebellar cortex neuron' and 'Mammalia Purkinje cell layer of cerebellar cortex (with-axons-in cerebellar nuclear complex Purkinje cell layer of cerebellar cortex) +AMPA +GABA-gated anionic channel +GABA projection neuron' has origLabel "Cerebellum Purkinje cell"

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[tgbugs]

To make sure I understand, 'granular layer of cerebellar cortex' UBERON:0002956 is the full composed term that is used for a number of these, and 'Purkinje cell layer of cerebellar cortex' UBERON:0002979 is distinct. A generic 'granular layer' isn't used and I don't think we even have one in the ontology, there are neocortical layers 1-6 in uberon, which I use for cell layers, but they are explicitly neocortical. The Paxinos parcellations have fully generic layer numbers that are completely orthogonal to the brain region.

I source the brain region terms directly from uberon if there isn't an abbreviated name. If we need improved naming to avoid confusion in cases like this we can start collecting lists of preferred terms for brain regions as part of our global naming convention rules.

[memartone]

It’s not a priority. Thanks for checking in.

On Jun 15, 2019, at 11:42 PM, Tom Gillespie notifications@github.com wrote:

To make sure I understand, 'granular layer of cerebellar cortex' UBERON:0002956 is the full composed term that is used for a number of these, and 'Purkinje cell layer of cerebellar cortex' UBERON:0002979 is distinct. A generic 'granular layer' isn't used and I don't think we even have one in the ontology, there are neocortical layers 1-6 in uberon, which I use for cell layers, but they are explicitly neocortical. The Paxinos parcellations have fully generic layer numbers that are completely orthogonal to the brain region.

I source the brain region terms directly from uberon if there isn't an abbreviated name. If we need improved naming to avoid confusion in cases like this we can start collecting lists of preferred terms for brain regions as part of our global naming convention rules.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/SciCrunch/NIF-Ontology/issues/170?email_source=notifications&email_token=ABSGOPJGAWCJQVXN5WSJP4LP2XOEJA5CNFSM4HYPZ6LKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXZGRYI#issuecomment-502425825, or mute the thread https://github.com/notifications/unsubscribe-auth/ABSGOPPI7QKKYW2VZPFILQTP2XOEJANCNFSM4HYPZ6LA.